#[cfg(target_family = "unix")]
use std::os::unix::prelude::*;
use std::{
    collections::HashMap,
    hash::Hash,
    path::{Path, PathBuf},
    time, vec,
};

use anyhow::{anyhow, bail, Context, Result};
use bstr::ByteSlice;
use diffy::{apply as diffy_apply, Line, Patch};
use git2_hooks::HookResult;
use regex::Regex;
use serde::Serialize;

use super::{
    branch::{
        self, Branch, BranchCreateRequest, BranchId, BranchOwnershipClaims, Hunk, OwnershipClaim,
    },
    branch_to_remote_branch, context, errors, target, Iterator, RemoteBranch,
    VirtualBranchesHandle,
};
use crate::{
    askpass::AskpassBroker,
    dedup::{dedup, dedup_fmt},
    gb_repository,
    git::{
        self,
        diff::{self, diff_files_to_hunks},
        show, Commit, Refname, RemoteRefname,
    },
    keys,
    project_repository::{self, conflicts, LogUntil},
    projects, reader, sessions, users,
};
use crate::{error::Error, git::diff::GitHunk};

type AppliedStatuses = Vec<(branch::Branch, HashMap<PathBuf, Vec<diff::GitHunk>>)>;

// this struct is a mapping to the view `Branch` type in Typescript
// found in src-tauri/src/routes/repo/[project_id]/types.ts
// it holds a materialized view for presentation purposes of the Branch struct in Rust
// which is our persisted data structure for virtual branches
//
// it is not persisted, it is only used for presentation purposes through the ipc
//
#[derive(Debug, PartialEq, Clone, Serialize)]
#[serde(rename_all = "camelCase")]
#[allow(clippy::struct_excessive_bools)]
pub struct VirtualBranch {
    pub id: BranchId,
    pub name: String,
    pub notes: String,
    pub active: bool,
    pub files: Vec<VirtualBranchFile>,
    pub commits: Vec<VirtualBranchCommit>,
    pub requires_force: bool, // does this branch require a force push to the upstream?
    pub conflicted: bool, // is this branch currently in a conflicted state (only for the workspace)
    pub order: usize,     // the order in which this branch should be displayed in the UI
    pub upstream: Option<RemoteBranch>, // the upstream branch where this branch pushes to, if any
    pub upstream_name: Option<String>, // the upstream branch where this branch will push to on next push
    pub base_current: bool, // is this vbranch based on the current base branch? if false, this needs to be manually merged with conflicts
    pub ownership: BranchOwnershipClaims,
    pub updated_at: u128,
    pub selected_for_changes: bool,
    pub head: git::Oid,
}

#[derive(Debug, PartialEq, Clone, Serialize)]
#[serde(rename_all = "camelCase")]
pub struct VirtualBranches {
    pub branches: Vec<VirtualBranch>,
    pub skipped_files: Vec<git::diff::FileDiff>,
}

// this is the struct that maps to the view `Commit` type in Typescript
// it is derived from walking the git commits between the `Branch.head` commit
// and the `Target.sha` commit, or, everything that is uniquely committed to
// the virtual branch we assign it to. an array of them are returned as part of
// the `VirtualBranch` struct
//
// it is not persisted, it is only used for presentation purposes through the ipc
//
#[derive(Debug, PartialEq, Clone, Serialize)]
#[serde(rename_all = "camelCase")]
pub struct VirtualBranchCommit {
    pub id: git::Oid,
    pub description: String,
    pub created_at: u128,
    pub author: Author,
    pub is_remote: bool,
    pub files: Vec<VirtualBranchFile>,
    pub is_integrated: bool,
    pub parent_ids: Vec<git::Oid>,
    pub branch_id: BranchId,
}

// this struct is a mapping to the view `File` type in Typescript
// found in src-tauri/src/routes/repo/[project_id]/types.ts
// it holds a materialized view for presentation purposes of one entry of the
// `Branch.ownership` vector in Rust. an array of them are returned as part of
// the `VirtualBranch` struct, which map to each entry of the `Branch.ownership` vector
//
// it is not persisted, it is only used for presentation purposes through the ipc
//
#[derive(Debug, PartialEq, Clone, Serialize)]
#[serde(rename_all = "camelCase")]
pub struct VirtualBranchFile {
    pub id: String,
    pub path: PathBuf,
    pub hunks: Vec<VirtualBranchHunk>,
    pub modified_at: u128,
    pub conflicted: bool,
    pub binary: bool,
    pub large: bool,
}

// this struct is a mapping to the view `Hunk` type in Typescript
// found in src-tauri/src/routes/repo/[project_id]/types.ts
// it holds a materialized view for presentation purposes of one entry of the
// each hunk in one `Branch.ownership` vector entry in Rust.
// an array of them are returned as part of the `VirtualBranchFile` struct
//
// it is not persisted, it is only used for presentation purposes through the ipc
//
#[derive(Debug, PartialEq, Clone, Serialize)]
#[serde(rename_all = "camelCase")]
pub struct VirtualBranchHunk {
    pub id: String,
    pub diff: String,
    pub modified_at: u128,
    pub file_path: PathBuf,
    pub hash: String,
    pub old_start: u32,
    pub start: u32,
    pub end: u32,
    pub binary: bool,
    pub locked: bool,
    pub locked_to: Option<git::Oid>,
    pub change_type: diff::ChangeType,
}

#[derive(Debug, Serialize, Hash, Clone, PartialEq, Eq)]
#[serde(rename_all = "camelCase")]
pub struct Author {
    pub name: String,
    pub email: String,
    pub gravatar_url: url::Url,
}

impl From<git::Signature<'_>> for Author {
    fn from(value: git::Signature) -> Self {
        let name = value.name().unwrap_or_default().to_string();
        let email = value.email().unwrap_or_default().to_string();

        let gravatar_url = url::Url::parse(&format!(
            "https://www.gravatar.com/avatar/{:x}?s=100&r=g&d=retro",
            md5::compute(email.to_lowercase())
        ))
        .unwrap();

        Author {
            name,
            email,
            gravatar_url,
        }
    }
}

pub fn normalize_branch_name(name: &str) -> String {
    let pattern = Regex::new("[^A-Za-z0-9_/.#]+").unwrap();
    pattern.replace_all(name, "-").to_string()
}

fn get_default_target(
    session_reader: &sessions::Reader,
    project: &projects::Project,
) -> Result<Option<target::Target>, reader::Error> {
    let target_reader = target::Reader::new(
        session_reader,
        VirtualBranchesHandle::new(&project.gb_dir()),
        project.use_toml_vbranches_state(),
    );
    match target_reader.read_default() {
        Ok(target) => Ok(Some(target)),
        Err(reader::Error::NotFound) => Ok(None),
        Err(error) => Err(error),
    }
}

pub fn apply_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    signing_key: Option<&keys::PrivateKey>,
    user: Option<&users::User>,
) -> Result<(), errors::ApplyBranchError> {
    if project_repository.is_resolving() {
        return Err(errors::ApplyBranchError::Conflict(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }
    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;

    let repo = &project_repository.git_repository;

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::ApplyBranchError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create branch writer")?;

    let mut branch = match branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .read(branch_id)
    {
        Ok(branch) => Ok(branch),
        Err(reader::Error::NotFound) => Err(errors::ApplyBranchError::BranchNotFound(
            errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            },
        )),
        Err(error) => Err(errors::ApplyBranchError::Other(error.into())),
    }?;

    if branch.applied {
        return Ok(());
    }

    let target_commit = repo
        .find_commit(default_target.sha)
        .context("failed to find target commit")?;
    let target_tree = target_commit.tree().context("failed to get target tree")?;

    // calculate the merge base and make sure it's the same as the target commit
    // if not, we need to merge or rebase the branch to get it up to date

    let merge_base = repo
        .merge_base(default_target.sha, branch.head)
        .context(format!(
            "failed to find merge base between {} and {}",
            default_target.sha, branch.head
        ))?;
    if merge_base != default_target.sha {
        // Branch is out of date, merge or rebase it
        let merge_base_tree = repo
            .find_commit(merge_base)
            .context(format!("failed to find merge base commit {}", merge_base))?
            .tree()
            .context("failed to find merge base tree")?;

        let branch_tree = repo
            .find_tree(branch.tree)
            .context("failed to find branch tree")?;

        let mut merge_index = repo
            .merge_trees(&merge_base_tree, &branch_tree, &target_tree)
            .context("failed to merge trees")?;

        if merge_index.has_conflicts() {
            // currently we can only deal with the merge problem branch
            for mut branch in super::get_status_by_branch(
                gb_repository,
                project_repository,
                Some(&target_commit.id()),
            )?
            .0
            .into_iter()
            .map(|(branch, _)| branch)
            .filter(|branch| branch.applied)
            {
                branch.applied = false;
                writer.write(&mut branch)?;
            }

            // apply the branch
            branch.applied = true;
            writer.write(&mut branch)?;

            // checkout the conflicts
            repo.checkout_index(&mut merge_index)
                .allow_conflicts()
                .conflict_style_merge()
                .force()
                .checkout()
                .context("failed to checkout index")?;

            // mark conflicts
            let conflicts = merge_index
                .conflicts()
                .context("failed to get merge index conflicts")?;
            let mut merge_conflicts = Vec::new();
            for path in conflicts.flatten() {
                if let Some(ours) = path.our {
                    let path = std::str::from_utf8(&ours.path)
                        .context("failed to convert path to utf8")?
                        .to_string();
                    merge_conflicts.push(path);
                }
            }
            conflicts::mark(
                project_repository,
                &merge_conflicts,
                Some(default_target.sha),
            )?;

            return Ok(());
        }

        let head_commit = repo
            .find_commit(branch.head)
            .context("failed to find head commit")?;

        let merged_branch_tree_oid = merge_index
            .write_tree_to(repo)
            .context("failed to write tree")?;

        let merged_branch_tree = repo
            .find_tree(merged_branch_tree_oid)
            .context("failed to find tree")?;

        let ok_with_force_push = project_repository.project().ok_with_force_push;
        if branch.upstream.is_some() && !ok_with_force_push {
            // branch was pushed to upstream, and user doesn't like force pushing.
            // create a merge commit to avoid the need of force pushing then.

            let new_branch_head = project_repository.commit(
                user,
                format!(
                    "Merged {}/{} into {}",
                    default_target.branch.remote(),
                    default_target.branch.branch(),
                    branch.name
                )
                .as_str(),
                &merged_branch_tree,
                &[&head_commit, &target_commit],
                signing_key,
            )?;

            // ok, update the virtual branch
            branch.head = new_branch_head;
            branch.tree = merged_branch_tree_oid;
            writer.write(&mut branch)?;
        } else {
            // branch was not pushed to upstream yet. attempt a rebase,
            let (_, committer) = project_repository.git_signatures(user)?;
            let mut rebase_options = git2::RebaseOptions::new();
            rebase_options.quiet(true);
            rebase_options.inmemory(true);
            let mut rebase = repo
                .rebase(
                    Some(branch.head),
                    Some(target_commit.id()),
                    None,
                    Some(&mut rebase_options),
                )
                .context("failed to rebase")?;

            let mut rebase_success = true;
            // check to see if these commits have already been pushed
            let mut last_rebase_head = branch.head;
            while rebase.next().is_some() {
                let index = rebase
                    .inmemory_index()
                    .context("failed to get inmemory index")?;
                if index.has_conflicts() {
                    rebase_success = false;
                    break;
                }

                if let Ok(commit_id) = rebase.commit(None, &committer.clone().into(), None) {
                    last_rebase_head = commit_id.into();
                } else {
                    rebase_success = false;
                    break;
                }
            }

            if rebase_success {
                // rebase worked out, rewrite the branch head
                rebase.finish(None).context("failed to finish rebase")?;
                branch.head = last_rebase_head;
                branch.tree = merged_branch_tree_oid;
            } else {
                // rebase failed, do a merge commit
                rebase.abort().context("failed to abort rebase")?;

                // get tree from merge_tree_oid
                let merge_tree = repo
                    .find_tree(merged_branch_tree_oid)
                    .context("failed to find tree")?;

                // commit the merge tree oid
                let new_branch_head = project_repository
                    .commit(
                        user,
                        format!(
                            "Merged {}/{} into {}",
                            default_target.branch.remote(),
                            default_target.branch.branch(),
                            branch.name
                        )
                        .as_str(),
                        &merge_tree,
                        &[&head_commit, &target_commit],
                        signing_key,
                    )
                    .context("failed to commit merge")?;

                branch.head = new_branch_head;
                branch.tree = merged_branch_tree_oid;
            }
        }
    }

    let wd_tree = project_repository.get_wd_tree()?;

    let branch_tree = repo
        .find_tree(branch.tree)
        .context("failed to find branch tree")?;

    // check index for conflicts
    let mut merge_index = repo
        .merge_trees(&target_tree, &wd_tree, &branch_tree)
        .context("failed to merge trees")?;

    if merge_index.has_conflicts() {
        return Err(errors::ApplyBranchError::BranchConflicts(*branch_id));
    }

    // apply the branch
    branch.applied = true;
    writer.write(&mut branch)?;

    ensure_selected_for_changes(
        &current_session_reader,
        &writer,
        project_repository.project(),
    )
    .context("failed to ensure selected for changes")?;

    // checkout the merge index
    repo.checkout_index(&mut merge_index)
        .force()
        .checkout()
        .context("failed to checkout index")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(())
}

pub fn unapply_ownership(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    ownership: &BranchOwnershipClaims,
) -> Result<(), errors::UnapplyOwnershipError> {
    if conflicts::is_resolving(project_repository) {
        return Err(errors::UnapplyOwnershipError::Conflict(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }

    let latest_session = gb_repository
        .get_latest_session()
        .context("failed to get or create current session")?
        .ok_or_else(|| {
            errors::UnapplyOwnershipError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let latest_session_reader = sessions::Reader::open(gb_repository, &latest_session)
        .context("failed to open current session")?;

    let default_target = get_default_target(&latest_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::UnapplyOwnershipError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let applied_branches = Iterator::new(
        &latest_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .filter(|b| b.applied)
    .collect::<Vec<_>>();

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    let (applied_statuses, _) = get_applied_status(
        gb_repository,
        project_repository,
        &integration_commit,
        &default_target.sha,
        applied_branches,
    )
    .context("failed to get status by branch")?;

    let hunks_to_unapply = applied_statuses
        .iter()
        .map(
            |(_branch, branch_files)| -> Result<Vec<(PathBuf, &diff::GitHunk)>> {
                let mut hunks_to_unapply = Vec::new();
                for (path, hunks) in branch_files {
                    let ownership_hunks: Vec<&Hunk> = ownership
                        .claims
                        .iter()
                        .filter(|o| o.file_path == *path)
                        .flat_map(|f| &f.hunks)
                        .collect();
                    for hunk in hunks {
                        if ownership_hunks.contains(&&Hunk::from(hunk)) {
                            hunks_to_unapply.push((path.clone(), hunk));
                        }
                    }
                }

                hunks_to_unapply.sort_by(|a, b| a.1.old_start.cmp(&b.1.old_start));

                Ok(hunks_to_unapply)
            },
        )
        .collect::<Result<Vec<_>>>()?
        .into_iter()
        .flatten()
        .collect::<Vec<_>>();

    let mut diff = HashMap::new();
    for h in hunks_to_unapply {
        if let Some(reversed_hunk) = diff::reverse_hunk(h.1) {
            diff.entry(h.0).or_insert_with(Vec::new).push(reversed_hunk);
        } else {
            return Err(errors::UnapplyOwnershipError::Other(anyhow::anyhow!(
                "failed to reverse hunk"
            )));
        }
    }

    let repo = &project_repository.git_repository;

    let target_commit = repo
        .find_commit(integration_commit)
        .context("failed to find target commit")?;

    let base_tree = target_commit.tree().context("failed to get target tree")?;
    let final_tree = applied_statuses.into_iter().fold(
        target_commit.tree().context("failed to get target tree"),
        |final_tree, status| {
            let final_tree = final_tree?;
            let tree_oid = write_tree(project_repository, &integration_commit, &status.1)?;
            let branch_tree = repo.find_tree(tree_oid)?;
            let mut result = repo.merge_trees(&base_tree, &final_tree, &branch_tree)?;
            let final_tree_oid = result.write_tree_to(repo)?;
            repo.find_tree(final_tree_oid)
                .context("failed to find tree")
        },
    )?;

    let final_tree_oid = write_tree_onto_tree(project_repository, &final_tree, &diff)?;
    let final_tree = repo
        .find_tree(final_tree_oid)
        .context("failed to find tree")?;

    repo.checkout_tree(&final_tree)
        .force()
        .remove_untracked()
        .checkout()
        .context("failed to checkout tree")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(())
}

// reset a file in the project to the index state
pub fn reset_files(
    project_repository: &project_repository::Repository,
    files: &Vec<String>,
) -> Result<(), errors::UnapplyOwnershipError> {
    if conflicts::is_resolving(project_repository) {
        return Err(errors::UnapplyOwnershipError::Conflict(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }

    // for each tree, we need to checkout the entry from the index at that path
    // or if it doesn't exist, remove the file from the working directory
    let repo = &project_repository.git_repository;
    let index = repo.index().context("failed to get index")?;
    for file in files {
        let entry = index.get_path(Path::new(file), 0);
        if entry.is_some() {
            repo.checkout_index_path(Path::new(file))
                .context("failed to checkout index")?;
        } else {
            // find the project root
            let project_root = &project_repository.project().path;
            let path = Path::new(file);
            //combine the project root with the file path
            let path = &project_root.join(path);
            std::fs::remove_file(path).context("failed to remove file")?;
        }
    }

    Ok(())
}

// to unapply a branch, we need to write the current tree out, then remove those file changes from the wd
pub fn unapply_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
) -> Result<Option<branch::Branch>, errors::UnapplyBranchError> {
    let session = &gb_repository
        .get_or_create_current_session()
        .context("failed to get or create currnt session")?;

    let current_session_reader =
        sessions::Reader::open(gb_repository, session).context("failed to open current session")?;

    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );

    let mut target_branch = branch_reader.read(branch_id).map_err(|error| match error {
        reader::Error::NotFound => {
            errors::UnapplyBranchError::BranchNotFound(errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            })
        }
        error => errors::UnapplyBranchError::Other(error.into()),
    })?;

    if !target_branch.applied {
        return Ok(Some(target_branch));
    }

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::UnapplyBranchError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let repo = &project_repository.git_repository;
    let target_commit = repo
        .find_commit(default_target.sha)
        .context("failed to find target commit")?;

    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;

    let final_tree = if conflicts::is_resolving(project_repository) {
        {
            target_branch.applied = false;
            target_branch.selected_for_changes = None;
            branch_writer.write(&mut target_branch)?;
        }
        conflicts::clear(project_repository).context("failed to clear conflicts")?;
        target_commit.tree().context("failed to get target tree")?
    } else {
        // if we are not resolving, we need to merge the rest of the applied branches
        let applied_branches = Iterator::new(
            &current_session_reader,
            VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
            project_repository.project().use_toml_vbranches_state(),
        )
        .context("failed to create branch iterator")?
        .collect::<Result<Vec<branch::Branch>, reader::Error>>()
        .context("failed to read virtual branches")?
        .into_iter()
        .filter(|b| b.applied)
        .collect::<Vec<_>>();

        let integration_commit =
            super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

        let (applied_statuses, _) = get_applied_status(
            gb_repository,
            project_repository,
            &integration_commit,
            &default_target.sha,
            applied_branches,
        )
        .context("failed to get status by branch")?;

        let status = applied_statuses
            .iter()
            .find(|(s, _)| s.id == target_branch.id)
            .context("failed to find status for branch");

        if let Ok((branch, files)) = status {
            update_conflict_markers(project_repository, files)?;
            if files.is_empty() && branch.head == default_target.sha {
                // if there is nothing to unapply, remove the branch straight away
                branch_writer
                    .delete(&target_branch)
                    .context("Failed to remove branch")?;

                ensure_selected_for_changes(
                    &current_session_reader,
                    &branch_writer,
                    project_repository.project(),
                )
                .context("failed to ensure selected for changes")?;

                project_repository.delete_branch_reference(&target_branch)?;
                return Ok(None);
            }

            target_branch.tree = write_tree(project_repository, &target_branch.head, files)?;
            target_branch.applied = false;
            target_branch.selected_for_changes = None;
            branch_writer.write(&mut target_branch)?;
        }

        let target_commit = repo
            .find_commit(default_target.sha)
            .context("failed to find target commit")?;

        // ok, update the wd with the union of the rest of the branches
        let base_tree = target_commit.tree().context("failed to get target tree")?;

        // go through the other applied branches and merge them into the final tree
        // then check that out into the working directory
        let final_tree = applied_statuses
            .into_iter()
            .filter(|(branch, _)| &branch.id != branch_id)
            .fold(
                target_commit.tree().context("failed to get target tree"),
                |final_tree, status| {
                    let final_tree = final_tree?;
                    let branch = status.0;
                    let tree_oid = write_tree(project_repository, &branch.head, &status.1)?;
                    let branch_tree = repo.find_tree(tree_oid)?;
                    let mut result = repo.merge_trees(&base_tree, &final_tree, &branch_tree)?;
                    let final_tree_oid = result.write_tree_to(repo)?;
                    repo.find_tree(final_tree_oid)
                        .context("failed to find tree")
                },
            )?;

        ensure_selected_for_changes(
            &current_session_reader,
            &branch_writer,
            project_repository.project(),
        )
        .context("failed to ensure selected for changes")?;

        final_tree
    };

    // checkout final_tree into the working directory
    repo.checkout_tree(&final_tree)
        .force()
        .remove_untracked()
        .checkout()
        .context("failed to checkout tree")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(Some(target_branch))
}

fn find_base_tree<'a>(
    repo: &'a git::Repository,
    branch_commit: &'a git::Commit<'a>,
    target_commit: &'a git::Commit<'a>,
) -> Result<git::Tree<'a>> {
    // find merge base between target_commit and branch_commit
    let merge_base = repo
        .merge_base(target_commit.id(), branch_commit.id())
        .context("failed to find merge base")?;
    // turn oid into a commit
    let merge_base_commit = repo
        .find_commit(merge_base)
        .context("failed to find merge base commit")?;
    let base_tree = merge_base_commit
        .tree()
        .context("failed to get base tree object")?;
    Ok(base_tree)
}

pub fn list_virtual_branches(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
) -> Result<(Vec<VirtualBranch>, bool, Vec<diff::FileDiff>), errors::ListVirtualBranchesError> {
    let mut branches: Vec<VirtualBranch> = Vec::new();

    let default_target = gb_repository
        .default_target()
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::ListVirtualBranchesError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    let (statuses, skipped_files) =
        get_status_by_branch(gb_repository, project_repository, Some(&integration_commit))?;
    let max_selected_for_changes = statuses
        .iter()
        .filter_map(|(branch, _)| branch.selected_for_changes)
        .max()
        .unwrap_or(-1);

    for (branch, files) in &statuses {
        let repo = &project_repository.git_repository;
        update_conflict_markers(project_repository, files)?;

        let upstream_branch = match branch
            .upstream
            .as_ref()
            .map(|name| repo.find_branch(&git::Refname::from(name)))
            .transpose()
        {
            Err(git::Error::NotFound(_)) => Ok(None),
            Err(error) => Err(error),
            Ok(branch) => Ok(branch),
        }
        .context(format!(
            "failed to find upstream branch for {}",
            branch.name
        ))?;

        let upstram_branch_commit = upstream_branch
            .as_ref()
            .map(git::Branch::peel_to_commit)
            .transpose()
            .context(format!(
                "failed to find upstream branch commit for {}",
                branch.name
            ))?;

        // find upstream commits if we found an upstream reference
        let mut pushed_commits = HashMap::new();
        if let Some(upstream) = &upstram_branch_commit {
            let merge_base =
                repo.merge_base(upstream.id(), default_target.sha)
                    .context(format!(
                        "failed to find merge base between {} and {}",
                        upstream.id(),
                        default_target.sha
                    ))?;
            for oid in project_repository.l(upstream.id(), LogUntil::Commit(merge_base))? {
                pushed_commits.insert(oid, true);
            }
        }

        let mut is_integrated = false;
        let mut is_remote = false;

        // find all commits on head that are not on target.sha
        let commits = project_repository
            .log(branch.head, LogUntil::Commit(default_target.sha))
            .context(format!("failed to get log for branch {}", branch.name))?
            .iter()
            .map(|commit| {
                is_remote = if is_remote {
                    is_remote
                } else {
                    pushed_commits.contains_key(&commit.id())
                };

                // only check for integration if we haven't already found an integration
                is_integrated = if is_integrated {
                    is_integrated
                } else {
                    is_commit_integrated(project_repository, &default_target, commit)?
                };

                commit_to_vbranch_commit(
                    project_repository,
                    branch,
                    commit,
                    is_integrated,
                    is_remote,
                )
            })
            .collect::<Result<Vec<_>>>()?;

        // if the branch is not applied, check to see if it's mergeable and up to date
        let mut base_current = true;
        if !branch.applied {
            // determine if this branch is up to date with the target/base
            let merge_base = repo
                .merge_base(default_target.sha, branch.head)
                .context("failed to find merge base")?;
            if merge_base != default_target.sha {
                base_current = false;
            }
        }

        let upstream = upstream_branch
            .map(|upstream_branch| branch_to_remote_branch(&upstream_branch))
            .transpose()?
            .flatten();

        let mut files = diffs_to_virtual_files(project_repository, files);
        files.sort_by(|a, b| {
            branch
                .ownership
                .claims
                .iter()
                .position(|o| o.file_path.eq(&a.path))
                .unwrap_or(999)
                .cmp(
                    &branch
                        .ownership
                        .claims
                        .iter()
                        .position(|id| id.file_path.eq(&b.path))
                        .unwrap_or(999),
                )
        });

        let requires_force = is_requires_force(project_repository, branch)?;
        let branch = VirtualBranch {
            id: branch.id,
            name: branch.name.clone(),
            notes: branch.notes.clone(),
            active: branch.applied,
            files,
            order: branch.order,
            commits,
            requires_force,
            upstream,
            upstream_name: branch
                .upstream
                .clone()
                .and_then(|r| Refname::from(r).branch().map(Into::into)),
            conflicted: conflicts::is_resolving(project_repository),
            base_current,
            ownership: branch.ownership.clone(),
            updated_at: branch.updated_timestamp_ms,
            selected_for_changes: branch.selected_for_changes == Some(max_selected_for_changes),
            head: branch.head,
        };
        branches.push(branch);
    }

    let branches = branches_with_large_files_abridged(branches);
    let mut branches = branches_with_hunk_locks(branches, project_repository)?;

    // If there no context lines are used internally, add them here, before returning to the UI
    if context_lines(project_repository) == 0 {
        for branch in &mut branches {
            branch.files = files_with_hunk_context(
                &project_repository.git_repository,
                branch.files.clone(),
                3,
                branch.head,
            )
            .context("failed to add hunk context")?;
        }
    }

    branches.sort_by(|a, b| a.order.cmp(&b.order));

    let uses_diff_context = project_repository
        .project()
        .use_diff_context
        .unwrap_or(false);
    Ok((branches, uses_diff_context, skipped_files))
}

fn branches_with_large_files_abridged(mut branches: Vec<VirtualBranch>) -> Vec<VirtualBranch> {
    for branch in &mut branches {
        for file in &mut branch.files {
            // Diffs larger than 500kb are considered large
            if file.hunks.iter().any(|hunk| hunk.diff.len() > 500_000) {
                file.large = true;
                file.hunks
                    .iter_mut()
                    .for_each(|hunk| hunk.diff = String::new());
            }
        }
    }
    branches
}

fn branches_with_hunk_locks(
    mut branches: Vec<VirtualBranch>,
    project_repository: &project_repository::Repository,
) -> Result<Vec<VirtualBranch>> {
    let all_commits: Vec<VirtualBranchCommit> = branches
        .clone()
        .iter()
        .filter(|branch| branch.active)
        .flat_map(|vbranch| vbranch.commits.clone())
        .collect();

    for commit in all_commits {
        let commit = project_repository.git_repository.find_commit(commit.id)?;
        let parent = commit.parent(0).context("failed to get parent commit")?;
        let commit_tree = commit.tree().context("failed to get commit tree")?;
        let parent_tree = parent.tree().context("failed to get parent tree")?;
        let commited_file_diffs = diff::trees(
            &project_repository.git_repository,
            &parent_tree,
            &commit_tree,
            context_lines(project_repository),
        )?;
        let commited_file_diffs = diff::diff_files_to_hunks(&commited_file_diffs);
        for branch in &mut branches {
            for file in &mut branch.files {
                for hunk in &mut file.hunks {
                    let locked =
                        commited_file_diffs
                            .get(&file.path)
                            .map_or(false, |committed_hunks| {
                                committed_hunks.iter().any(|committed_hunk| {
                                    joined(
                                        committed_hunk.new_start,
                                        committed_hunk.new_start + committed_hunk.new_lines,
                                        hunk.start,
                                        hunk.end,
                                    )
                                })
                            });
                    if locked {
                        hunk.locked = true;
                        hunk.locked_to = Some(commit.id());
                    }
                }
            }
        }
    }
    Ok(branches)
}

fn joined(start_a: u32, end_a: u32, start_b: u32, end_b: u32) -> bool {
    ((start_a >= start_b && start_a <= end_b) || (end_a >= start_b && end_a <= end_b))
        || ((start_b >= start_a && start_b <= end_a) || (end_b >= start_a && end_b <= end_a))
}

fn files_with_hunk_context(
    repository: &git::Repository,
    mut files: Vec<VirtualBranchFile>,
    context_lines: usize,
    branch_head: git::Oid,
) -> Result<Vec<VirtualBranchFile>> {
    for file in &mut files {
        if file.binary {
            continue;
        }
        // Get file content as it looked before the diffs
        let branch_head_commit = repository.find_commit(branch_head)?;
        let head_tree = branch_head_commit.tree()?;
        let file_content_before =
            show::show_file_at_tree(repository, file.path.clone(), &head_tree)
                .context("failed to get file contents at base")?;
        let file_lines_before = file_content_before.split('\n').collect::<Vec<_>>();

        // Update each hunk with contex lines before & after
        file.hunks = file
            .hunks
            .iter()
            .map(|hunk| {
                if hunk.diff.is_empty() {
                    // noop on empty diff
                    hunk.clone()
                } else {
                    let hunk_with_ctx = context::hunk_with_context(
                        &hunk.diff,
                        hunk.old_start as usize,
                        hunk.start as usize,
                        hunk.binary,
                        context_lines,
                        &file_lines_before,
                        hunk.change_type,
                    );
                    to_virtual_branch_hunk(hunk.clone(), hunk_with_ctx)
                }
            })
            .collect::<Vec<VirtualBranchHunk>>();
    }
    Ok(files)
}

fn to_virtual_branch_hunk(
    mut hunk: VirtualBranchHunk,
    diff_with_context: diff::GitHunk,
) -> VirtualBranchHunk {
    hunk.diff = diff_with_context.diff;
    hunk.start = diff_with_context.new_start;
    hunk.end = diff_with_context.new_start + diff_with_context.new_lines;
    hunk
}

fn is_requires_force(
    project_repository: &project_repository::Repository,
    branch: &branch::Branch,
) -> Result<bool> {
    let upstream = if let Some(upstream) = &branch.upstream {
        upstream
    } else {
        return Ok(false);
    };

    let reference = match project_repository
        .git_repository
        .refname_to_id(&upstream.to_string())
    {
        Ok(reference) => reference,
        Err(git::Error::NotFound(_)) => return Ok(false),
        Err(other) => return Err(other).context("failed to find upstream reference"),
    };

    let upstream_commit = project_repository
        .git_repository
        .find_commit(reference)
        .context("failed to find upstream commit")?;

    let merge_base = project_repository
        .git_repository
        .merge_base(upstream_commit.id(), branch.head)?;

    Ok(merge_base != upstream_commit.id())
}

fn list_virtual_commit_files(
    project_repository: &project_repository::Repository,
    commit: &git::Commit,
) -> Result<Vec<VirtualBranchFile>> {
    if commit.parent_count() == 0 {
        return Ok(vec![]);
    }
    let parent = commit.parent(0).context("failed to get parent commit")?;
    let commit_tree = commit.tree().context("failed to get commit tree")?;
    let parent_tree = parent.tree().context("failed to get parent tree")?;
    let diff = diff::trees(
        &project_repository.git_repository,
        &parent_tree,
        &commit_tree,
        context_lines(project_repository),
    )?;
    let diff = diff::diff_files_to_hunks(&diff);
    let hunks_by_filepath = virtual_hunks_by_filepath(&project_repository.project().path, &diff);
    Ok(virtual_hunks_to_virtual_files(
        project_repository,
        &hunks_by_filepath
            .values()
            .flatten()
            .cloned()
            .collect::<Vec<_>>(),
    ))
}

fn commit_to_vbranch_commit(
    repository: &project_repository::Repository,
    branch: &branch::Branch,
    commit: &git::Commit,
    is_integrated: bool,
    is_remote: bool,
) -> Result<VirtualBranchCommit> {
    let timestamp = u128::try_from(commit.time().seconds())?;
    let signature = commit.author();
    let message = commit.message().unwrap().to_string();

    let files =
        list_virtual_commit_files(repository, commit).context("failed to list commit files")?;

    let parent_ids = commit.parents()?.iter().map(Commit::id).collect::<Vec<_>>();

    let commit = VirtualBranchCommit {
        id: commit.id(),
        created_at: timestamp * 1000,
        author: Author::from(signature),
        description: message,
        is_remote,
        files,
        is_integrated,
        parent_ids,
        branch_id: branch.id,
    };

    Ok(commit)
}

pub fn create_virtual_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    create: &BranchCreateRequest,
) -> Result<branch::Branch, errors::CreateVirtualBranchError> {
    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create currnt session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::CreateVirtualBranchError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let commit = project_repository
        .git_repository
        .find_commit(default_target.sha)
        .context("failed to find default target commit")?;

    let tree = commit
        .tree()
        .context("failed to find defaut target commit tree")?;

    let mut all_virtual_branches = Iterator::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?;
    all_virtual_branches.sort_by_key(|branch| branch.order);

    let order = create
        .order
        .unwrap_or(all_virtual_branches.len())
        .clamp(0, all_virtual_branches.len());

    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;

    let selected_for_changes = if let Some(selected_for_changes) = create.selected_for_changes {
        if selected_for_changes {
            for mut other_branch in Iterator::new(
                &current_session_reader,
                VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
                project_repository.project().use_toml_vbranches_state(),
            )
            .context("failed to create branch iterator")?
            .collect::<Result<Vec<branch::Branch>, reader::Error>>()
            .context("failed to read virtual branches")?
            {
                other_branch.selected_for_changes = None;
                branch_writer.write(&mut other_branch)?;
            }
            Some(chrono::Utc::now().timestamp_millis())
        } else {
            None
        }
    } else {
        (!all_virtual_branches
            .iter()
            .any(|b| b.selected_for_changes.is_some()))
        .then_some(chrono::Utc::now().timestamp_millis())
    };

    // make space for the new branch
    for (i, branch) in all_virtual_branches.iter().enumerate() {
        let mut branch = branch.clone();
        let new_order = if i < order { i } else { i + 1 };
        if branch.order != new_order {
            branch.order = new_order;
            branch_writer
                .write(&mut branch)
                .context("failed to write branch")?;
        }
    }

    let now = time::UNIX_EPOCH
        .elapsed()
        .context("failed to get elapsed time")?
        .as_millis();

    let name = dedup(
        &all_virtual_branches
            .iter()
            .map(|b| b.name.as_str())
            .collect::<Vec<_>>(),
        create
            .name
            .as_ref()
            .unwrap_or(&"Virtual branch".to_string()),
    );

    let mut branch = Branch {
        id: BranchId::generate(),
        name,
        notes: String::new(),
        applied: true,
        upstream: None,
        upstream_head: None,
        tree: tree.id(),
        head: default_target.sha,
        created_timestamp_ms: now,
        updated_timestamp_ms: now,
        ownership: BranchOwnershipClaims::default(),
        order,
        selected_for_changes,
    };

    if let Some(ownership) = &create.ownership {
        set_ownership(
            &current_session_reader,
            &branch_writer,
            &mut branch,
            ownership,
            project_repository.project(),
        )
        .context("failed to set ownership")?;
    }

    branch_writer
        .write(&mut branch)
        .context("failed to write branch")?;

    project_repository.add_branch_reference(&branch)?;

    Ok(branch)
}

pub fn merge_virtual_branch_upstream(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    signing_key: Option<&keys::PrivateKey>,
    user: Option<&users::User>,
) -> Result<(), errors::MergeVirtualBranchUpstreamError> {
    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::MergeVirtualBranchUpstreamError::Conflict(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;

    // get the branch
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let mut branch = match branch_reader.read(branch_id) {
        Ok(branch) => Ok(branch),
        Err(reader::Error::NotFound) => Err(
            errors::MergeVirtualBranchUpstreamError::BranchNotFound(errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            }),
        ),
        Err(error) => Err(errors::MergeVirtualBranchUpstreamError::Other(error.into())),
    }?;

    // check if the branch upstream can be merged into the wd cleanly
    let repo = &project_repository.git_repository;

    // get upstream from the branch and find the remote branch
    let mut upstream_commit = None;
    let upstream_branch = branch
        .upstream
        .as_ref()
        .context("no upstream branch found")?;
    if let Ok(upstream_oid) = repo.refname_to_id(&upstream_branch.to_string()) {
        if let Ok(upstream_commit_obj) = repo.find_commit(upstream_oid) {
            upstream_commit = Some(upstream_commit_obj);
        }
    }

    // if there is no upstream commit, then there is nothing to do
    if upstream_commit.is_none() {
        // no upstream commit, no merge to be done
        return Ok(());
    }

    // there is an upstream commit, so lets check it out
    let upstream_commit = upstream_commit.unwrap();
    let remote_tree = upstream_commit.tree().context("failed to get tree")?;

    if upstream_commit.id() == branch.head {
        // upstream is already merged, nothing to do
        return Ok(());
    }

    // if any other branches are applied, unapply them
    let applied_branches = Iterator::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .filter(|b| b.applied)
    .filter(|b| b.id != *branch_id)
    .collect::<Vec<_>>();

    // unapply all other branches
    for other_branch in applied_branches {
        unapply_branch(gb_repository, project_repository, &other_branch.id)
            .context("failed to unapply branch")?;
    }

    // get merge base from remote branch commit and target commit
    let merge_base = repo
        .merge_base(upstream_commit.id(), branch.head)
        .context("failed to find merge base")?;
    let merge_tree = repo
        .find_commit(merge_base)
        .and_then(|c| c.tree())
        .context(format!(
            "failed to find merge base commit {} tree",
            merge_base
        ))?;

    // get wd tree
    let wd_tree = project_repository.get_wd_tree()?;

    // try to merge our wd tree with the upstream tree
    let mut merge_index = repo
        .merge_trees(&merge_tree, &wd_tree, &remote_tree)
        .context("failed to merge trees")?;

    if merge_index.has_conflicts() {
        // checkout the conflicts
        repo.checkout_index(&mut merge_index)
            .allow_conflicts()
            .conflict_style_merge()
            .force()
            .checkout()
            .context("failed to checkout index")?;

        // mark conflicts
        let conflicts = merge_index.conflicts().context("failed to get conflicts")?;
        let mut merge_conflicts = Vec::new();
        for path in conflicts.flatten() {
            if let Some(ours) = path.our {
                let path = std::str::from_utf8(&ours.path)
                    .context("failed to convert path to utf8")?
                    .to_string();
                merge_conflicts.push(path);
            }
        }
        conflicts::mark(
            project_repository,
            &merge_conflicts,
            Some(upstream_commit.id()),
        )?;
    } else {
        let merge_tree_oid = merge_index
            .write_tree_to(repo)
            .context("failed to write tree")?;
        let merge_tree = repo
            .find_tree(merge_tree_oid)
            .context("failed to find merge tree")?;
        let branch_writer = branch::Writer::new(
            gb_repository,
            VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        )
        .context("failed to create writer")?;

        if *project_repository.project().ok_with_force_push {
            // attempt a rebase
            let (_, committer) = project_repository.git_signatures(user)?;
            let mut rebase_options = git2::RebaseOptions::new();
            rebase_options.quiet(true);
            rebase_options.inmemory(true);
            let mut rebase = repo
                .rebase(
                    Some(branch.head),
                    Some(upstream_commit.id()),
                    None,
                    Some(&mut rebase_options),
                )
                .context("failed to rebase")?;

            let mut rebase_success = true;
            // check to see if these commits have already been pushed
            let mut last_rebase_head = upstream_commit.id();
            while rebase.next().is_some() {
                let index = rebase
                    .inmemory_index()
                    .context("failed to get inmemory index")?;
                if index.has_conflicts() {
                    rebase_success = false;
                    break;
                }

                if let Ok(commit_id) = rebase.commit(None, &committer.clone().into(), None) {
                    last_rebase_head = commit_id.into();
                } else {
                    rebase_success = false;
                    break;
                }
            }

            if rebase_success {
                // rebase worked out, rewrite the branch head
                rebase.finish(None).context("failed to finish rebase")?;

                project_repository
                    .git_repository
                    .checkout_tree(&merge_tree)
                    .force()
                    .checkout()
                    .context("failed to checkout tree")?;

                branch.head = last_rebase_head;
                branch.tree = merge_tree_oid;
                branch_writer.write(&mut branch)?;
                super::integration::update_gitbutler_integration(
                    gb_repository,
                    project_repository,
                )?;

                return Ok(());
            }

            rebase.abort().context("failed to abort rebase")?;
        }

        let head_commit = repo
            .find_commit(branch.head)
            .context("failed to find head commit")?;

        let new_branch_head = project_repository.commit(
            user,
            format!(
                "Merged {}/{} into {}",
                upstream_branch.remote(),
                upstream_branch.branch(),
                branch.name
            )
            .as_str(),
            &merge_tree,
            &[&head_commit, &upstream_commit],
            signing_key,
        )?;

        // checkout the merge tree
        repo.checkout_tree(&merge_tree)
            .force()
            .checkout()
            .context("failed to checkout tree")?;

        // write the branch data
        branch.head = new_branch_head;
        branch.tree = merge_tree_oid;
        branch_writer.write(&mut branch)?;
    }

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(())
}

pub fn update_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_update: branch::BranchUpdateRequest,
) -> Result<branch::Branch, errors::UpdateBranchError> {
    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create currnt session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;

    let mut branch = branch_reader
        .read(&branch_update.id)
        .map_err(|error| match error {
            reader::Error::NotFound => {
                errors::UpdateBranchError::BranchNotFound(errors::BranchNotFound {
                    project_id: project_repository.project().id,
                    branch_id: branch_update.id,
                })
            }
            _ => errors::UpdateBranchError::Other(error.into()),
        })?;

    if let Some(ownership) = branch_update.ownership {
        set_ownership(
            &current_session_reader,
            &branch_writer,
            &mut branch,
            &ownership,
            project_repository.project(),
        )
        .context("failed to set ownership")?;
    }

    if let Some(name) = branch_update.name {
        let all_virtual_branches = Iterator::new(
            &current_session_reader,
            VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
            project_repository.project().use_toml_vbranches_state(),
        )
        .context("failed to create branch iterator")?
        .collect::<Result<Vec<branch::Branch>, reader::Error>>()
        .context("failed to read virtual branches")?;

        project_repository.delete_branch_reference(&branch)?;

        branch.name = dedup(
            &all_virtual_branches
                .iter()
                .map(|b| b.name.as_str())
                .collect::<Vec<_>>(),
            &name,
        );

        project_repository.add_branch_reference(&branch)?;
    };

    if let Some(updated_upstream) = branch_update.upstream {
        let default_target =
            get_default_target(&current_session_reader, project_repository.project())
                .context("failed to get default target")?
                .ok_or_else(|| {
                    errors::UpdateBranchError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                        project_id: project_repository.project().id,
                    })
                })?;
        let remote_branch = format!(
            "refs/remotes/{}/{}",
            default_target.branch.remote(),
            normalize_branch_name(&updated_upstream)
        )
        .parse::<git::RemoteRefname>()
        .unwrap();
        branch.upstream = Some(remote_branch);
    };

    if let Some(notes) = branch_update.notes {
        branch.notes = notes;
    };

    if let Some(order) = branch_update.order {
        branch.order = order;
    };

    if let Some(selected_for_changes) = branch_update.selected_for_changes {
        branch.selected_for_changes = if selected_for_changes {
            for mut other_branch in Iterator::new(
                &current_session_reader,
                VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
                project_repository.project().use_toml_vbranches_state(),
            )
            .context("failed to create branch iterator")?
            .collect::<Result<Vec<branch::Branch>, reader::Error>>()
            .context("failed to read virtual branches")?
            .into_iter()
            .filter(|b| b.id != branch.id)
            {
                other_branch.selected_for_changes = None;
                branch_writer.write(&mut other_branch)?;
            }
            Some(chrono::Utc::now().timestamp_millis())
        } else {
            None
        };
    };

    branch_writer
        .write(&mut branch)
        .context("failed to write target branch")?;

    Ok(branch)
}

pub fn delete_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
) -> Result<(), Error> {
    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create currnt session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;

    let branch = match branch_reader.read(branch_id) {
        Ok(branch) => Ok(branch),
        Err(reader::Error::NotFound) => return Ok(()),
        Err(error) => Err(error),
    }
    .context("failed to read branch")?;

    if branch.applied && unapply_branch(gb_repository, project_repository, branch_id)?.is_none() {
        return Ok(());
    }

    branch_writer
        .delete(&branch)
        .context("Failed to remove branch")?;

    project_repository.delete_branch_reference(&branch)?;

    ensure_selected_for_changes(
        &current_session_reader,
        &branch_writer,
        project_repository.project(),
    )
    .context("failed to ensure selected for changes")?;

    Ok(())
}

fn ensure_selected_for_changes(
    current_session_reader: &sessions::Reader,
    branch_writer: &branch::Writer,
    project: &projects::Project,
) -> Result<()> {
    let mut applied_branches = Iterator::new(
        current_session_reader,
        VirtualBranchesHandle::new(&project.gb_dir()),
        project.use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .filter(|b| b.applied)
    .collect::<Vec<_>>();

    if applied_branches.is_empty() {
        println!("no applied branches");
        return Ok(());
    }

    if applied_branches
        .iter()
        .any(|b| b.selected_for_changes.is_some())
    {
        println!("some branches already selected for changes");
        return Ok(());
    }

    applied_branches.sort_by_key(|branch| branch.order);

    applied_branches[0].selected_for_changes = Some(chrono::Utc::now().timestamp_millis());
    branch_writer.write(&mut applied_branches[0])?;
    Ok(())
}

fn set_ownership(
    session_reader: &sessions::Reader,
    branch_writer: &branch::Writer,
    target_branch: &mut branch::Branch,
    ownership: &branch::BranchOwnershipClaims,
    project: &projects::Project,
) -> Result<()> {
    if target_branch.ownership.eq(ownership) {
        // nothing to update
        return Ok(());
    }

    let virtual_branches = Iterator::new(
        session_reader,
        VirtualBranchesHandle::new(&project.gb_dir()),
        project.use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?;

    let mut claim_outcomes =
        branch::reconcile_claims(virtual_branches, target_branch, &ownership.claims)?;
    for claim_outcome in &mut claim_outcomes {
        if !claim_outcome.removed_claims.is_empty() {
            branch_writer
                .write(&mut claim_outcome.updated_branch)
                .context("failed to write ownership for branch".to_string())?;
        }
    }

    // Updates the claiming branch that was passed as mutable state with the new ownership claims
    // TODO: remove mutable reference to target_branch
    target_branch.ownership = ownership.clone();

    Ok(())
}

fn get_mtime(cache: &mut HashMap<PathBuf, u128>, file_path: &PathBuf) -> u128 {
    if let Some(mtime) = cache.get(file_path) {
        *mtime
    } else {
        let mtime = file_path
            .metadata()
            .map_or_else(
                |_| time::SystemTime::now(),
                |metadata| {
                    metadata
                        .modified()
                        .or(metadata.created())
                        .unwrap_or_else(|_| time::SystemTime::now())
                },
            )
            .duration_since(time::UNIX_EPOCH)
            .unwrap()
            .as_millis();
        cache.insert(file_path.clone(), mtime);
        mtime
    }
}

pub fn virtual_hunks_by_filepath(
    project_path: &Path,
    diff: &HashMap<PathBuf, Vec<diff::GitHunk>>,
) -> HashMap<PathBuf, Vec<VirtualBranchHunk>> {
    let mut mtimes: HashMap<PathBuf, u128> = HashMap::new();
    diff.iter()
        .map(|(file_path, hunks)| {
            let hunks = hunks
                .iter()
                .map(|hunk| VirtualBranchHunk {
                    id: format!("{}-{}", hunk.new_start, hunk.new_start + hunk.new_lines),
                    modified_at: get_mtime(&mut mtimes, &project_path.join(file_path)),
                    file_path: file_path.clone(),
                    diff: hunk.diff.clone(),
                    old_start: hunk.old_start,
                    start: hunk.new_start,
                    end: hunk.new_start + hunk.new_lines,
                    binary: hunk.binary,
                    hash: Hunk::hash(&hunk.diff),
                    locked: false,
                    locked_to: None,
                    change_type: hunk.change_type,
                })
                .collect::<Vec<_>>();
            (file_path.clone(), hunks)
        })
        .collect::<HashMap<_, _>>()
}

pub type BranchStatus = HashMap<PathBuf, Vec<diff::GitHunk>>;

// list the virtual branches and their file statuses (statusi?)
#[allow(clippy::type_complexity)]
pub fn get_status_by_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    integration_commit: Option<&git::Oid>,
) -> Result<(Vec<(branch::Branch, BranchStatus)>, Vec<diff::FileDiff>)> {
    let latest_session = gb_repository
        .get_latest_session()
        .context("failed to get latest session")?
        .context("latest session not found")?;
    let session_reader = sessions::Reader::open(gb_repository, &latest_session)
        .context("failed to open current session")?;

    let default_target = match get_default_target(&session_reader, project_repository.project())
        .context("failed to read default target")?
    {
        Some(target) => target,
        None => {
            return Ok((vec![], vec![]));
        }
    };

    let virtual_branches = Iterator::new(
        &session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?;

    let applied_virtual_branches = virtual_branches
        .iter()
        .filter(|branch| branch.applied)
        .cloned()
        .collect::<Vec<_>>();

    let (applied_status, skipped_files) = get_applied_status(
        gb_repository,
        project_repository,
        // TODO: Keep this optional or update lots of tests?
        integration_commit.unwrap_or(&default_target.sha),
        &default_target.sha,
        applied_virtual_branches,
    )?;

    let non_applied_virtual_branches = virtual_branches
        .into_iter()
        .filter(|branch| !branch.applied)
        .collect::<Vec<_>>();

    let non_applied_status =
        get_non_applied_status(project_repository, non_applied_virtual_branches)?;

    Ok((
        applied_status
            .into_iter()
            .chain(non_applied_status)
            .collect(),
        skipped_files,
    ))
}

// given a list of non applied virtual branches, return the status of each file, comparing the default target with
// virtual branch latest tree
//
// ownerships are not taken into account here, as they are not relevant for non applied branches
fn get_non_applied_status(
    project_repository: &project_repository::Repository,
    virtual_branches: Vec<branch::Branch>,
) -> Result<Vec<(branch::Branch, BranchStatus)>> {
    virtual_branches
        .into_iter()
        .map(
            |branch| -> Result<(branch::Branch, HashMap<PathBuf, Vec<diff::GitHunk>>)> {
                if branch.applied {
                    bail!("branch {} is applied", branch.name);
                }
                let branch_tree = project_repository
                    .git_repository
                    .find_tree(branch.tree)
                    .context(format!("failed to find tree {}", branch.tree))?;

                let head_tree = project_repository
                    .git_repository
                    .find_commit(branch.head)
                    .context("failed to find target commit")?
                    .tree()
                    .context("failed to find target tree")?;

                let diff = diff::trees(
                    &project_repository.git_repository,
                    &head_tree,
                    &branch_tree,
                    context_lines(project_repository),
                )?;

                Ok((branch, diff::diff_files_to_hunks(&diff)))
            },
        )
        .collect::<Result<Vec<_>>>()
}

// given a list of applied virtual branches, return the status of each file, comparing the default target with
// the working directory
//
// ownerships are updated if nessessary
fn get_applied_status(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    integration_commit: &git::Oid,
    target_sha: &git::Oid,
    mut virtual_branches: Vec<branch::Branch>,
) -> Result<(AppliedStatuses, Vec<diff::FileDiff>)> {
    let base_file_diffs = diff::workdir(
        &project_repository.git_repository,
        integration_commit,
        context_lines(project_repository),
    )
    .context("failed to diff workdir")?;

    let mut base_diffs: HashMap<PathBuf, Vec<git::diff::GitHunk>> =
        diff_files_to_hunks(&base_file_diffs);
    let mut skipped_files: Vec<diff::FileDiff> = Vec::new();
    for (_, file_diff) in base_file_diffs {
        if file_diff.skipped {
            skipped_files.push(file_diff);
        }
    }

    // sort by order, so that the default branch is first (left in the ui)
    virtual_branches.sort_by(|a, b| a.order.cmp(&b.order));

    if virtual_branches.is_empty() && !base_diffs.is_empty() {
        // no virtual branches, but hunks: create default branch
        virtual_branches = vec![create_virtual_branch(
            gb_repository,
            project_repository,
            &BranchCreateRequest::default(),
        )
        .context("failed to create default branch")?];
    }

    // align branch ownership to the real hunks:
    // - update shifted hunks
    // - remove non existent hunks

    let mut diffs_by_branch: HashMap<BranchId, HashMap<PathBuf, Vec<diff::GitHunk>>> =
        virtual_branches
            .iter()
            .map(|branch| (branch.id, HashMap::new()))
            .collect();

    let mut mtimes = HashMap::new();

    let mut git_hunk_map = HashMap::new();

    for branch in &virtual_branches {
        if !branch.applied {
            bail!("branch {} is not applied", branch.name);
        }
        let commits = project_repository.log(branch.head, LogUntil::Commit(*target_sha));
        if let Ok(commits) = commits {
            for commit in commits {
                let commit = project_repository
                    .git_repository
                    .find_commit(commit.id())
                    .unwrap();
                let parent = commit
                    .parent(0)
                    .context("failed to get parent commit")
                    .unwrap();
                let commit_tree = commit.tree().context("failed to get commit tree").unwrap();
                let parent_tree = parent.tree().context("failed to get parent tree").unwrap();
                let commited_file_diffs = diff::trees(
                    &project_repository.git_repository,
                    &parent_tree,
                    &commit_tree,
                    context_lines(project_repository),
                );
                let commited_file_diffs = diff::diff_files_to_hunks(&commited_file_diffs.unwrap());
                for (path, committed_git_hunks) in commited_file_diffs.iter() {
                    if let Some(uncommitted_git_hunks) = base_diffs.get_mut(path) {
                        for uncommitted_git_hunk in uncommitted_git_hunks {
                            for committed_git_hunk in committed_git_hunks {
                                if joined(
                                    uncommitted_git_hunk.new_start,
                                    uncommitted_git_hunk.new_start + uncommitted_git_hunk.new_lines,
                                    committed_git_hunk.new_start,
                                    committed_git_hunk.new_start + committed_git_hunk.new_lines,
                                ) {
                                    let hash = Hunk::hash(&uncommitted_git_hunk.diff);
                                    git_hunk_map.insert(hash, branch.id);
                                }
                            }
                        }
                    }
                }
            }
        }
    }

    for branch in &mut virtual_branches {
        if !branch.applied {
            bail!("branch {} is not applied", branch.name);
        }

        let old_claims = branch.ownership.claims.clone();
        let new_claims = old_claims
            .iter()
            .filter_map(|claim| {
                let git_diff_hunks = match base_diffs.get_mut(&claim.file_path) {
                    None => return None,
                    Some(hunks) => hunks,
                };

                let mtime = get_mtime(&mut mtimes, &claim.file_path);

                let claimed_hunks: Vec<Hunk> = claim
                    .hunks
                    .iter()
                    .filter_map(|claimed_hunk| {
                        // if any of the current hunks intersects with the owned hunk, we want to keep it
                        for (i, git_diff_hunk) in git_diff_hunks.iter().enumerate() {
                            let hash = Hunk::hash(&git_diff_hunk.diff);
                            if let Some(locked_to) = git_hunk_map.get(&hash) {
                                if locked_to != &branch.id {
                                    return None;
                                }
                            }
                            if claimed_hunk.eq(&Hunk::from(git_diff_hunk)) {
                                // try to re-use old timestamp
                                let timestamp = claimed_hunk.timestam_ms().unwrap_or(mtime);
                                diffs_by_branch
                                    .entry(branch.id)
                                    .or_default()
                                    .entry(claim.file_path.clone())
                                    .or_default()
                                    .push(git_diff_hunk.clone());

                                git_diff_hunks.remove(i);
                                return Some(
                                    claimed_hunk
                                        .with_timestamp(timestamp)
                                        .with_hash(hash.as_str()),
                                );
                            } else if claimed_hunk.intersects(git_diff_hunk) {
                                diffs_by_branch
                                    .entry(branch.id)
                                    .or_default()
                                    .entry(claim.file_path.clone())
                                    .or_default()
                                    .insert(0, git_diff_hunk.clone());
                                let updated_hunk = Hunk {
                                    start: git_diff_hunk.new_start,
                                    end: git_diff_hunk.new_start + git_diff_hunk.new_lines,
                                    timestamp_ms: Some(mtime),
                                    hash: Some(hash.clone()),
                                };
                                git_diff_hunks.remove(i);
                                return Some(updated_hunk);
                            }
                        }
                        None
                    })
                    .collect();

                if claimed_hunks.is_empty() {
                    // No need for an empty claim
                    None
                } else {
                    Some(OwnershipClaim {
                        file_path: claim.file_path.clone(),
                        hunks: claimed_hunks,
                    })
                }
            })
            .collect();

        branch.ownership = BranchOwnershipClaims { claims: new_claims };
    }

    let max_selected_for_changes = virtual_branches
        .iter()
        .filter_map(|b| b.selected_for_changes)
        .max()
        .unwrap_or(-1);
    let default_vbranch_pos = virtual_branches
        .iter()
        .position(|b| b.selected_for_changes == Some(max_selected_for_changes))
        .unwrap_or(0);

    for (filepath, hunks) in base_diffs {
        for hunk in hunks {
            let hash = Hunk::hash(&hunk.diff);
            let vbranch_pos = if let Some(locked_to) = git_hunk_map.get(&hash) {
                let p = virtual_branches.iter().position(|vb| vb.id == *locked_to);
                match p {
                    Some(p) => p,
                    _ => default_vbranch_pos,
                }
            } else {
                default_vbranch_pos
            };

            virtual_branches[vbranch_pos]
                .ownership
                .put(&OwnershipClaim {
                    file_path: filepath.clone(),
                    hunks: vec![Hunk::from(&hunk)
                        .with_timestamp(get_mtime(&mut mtimes, &filepath))
                        .with_hash(Hunk::hash(hunk.diff.as_str()).as_str())],
                });

            diffs_by_branch
                .entry(virtual_branches[vbranch_pos].id)
                .or_default()
                .entry(filepath.clone())
                .or_default()
                .push(hunk.clone());
        }
    }

    let mut hunks_by_branch = diffs_by_branch
        .into_iter()
        .map(|(branch_id, hunks)| {
            (
                virtual_branches
                    .iter()
                    .find(|b| b.id.eq(&branch_id))
                    .unwrap()
                    .clone(),
                hunks,
            )
        })
        .collect::<Vec<_>>();

    // write updated state if not resolving
    if !project_repository.is_resolving() {
        let branch_writer = branch::Writer::new(
            gb_repository,
            VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        )
        .context("failed to create writer")?;
        for (vbranch, files) in &mut hunks_by_branch {
            vbranch.tree = write_tree(project_repository, integration_commit, files)?;
            branch_writer
                .write(vbranch)
                .context(format!("failed to write virtual branch {}", vbranch.name))?;
        }
    }

    Ok((hunks_by_branch, skipped_files))
}

fn virtual_hunks_to_virtual_files(
    project_repository: &project_repository::Repository,
    hunks: &[VirtualBranchHunk],
) -> Vec<VirtualBranchFile> {
    hunks
        .iter()
        .fold(HashMap::<PathBuf, Vec<_>>::new(), |mut acc, hunk| {
            acc.entry(hunk.file_path.clone())
                .or_default()
                .push(hunk.clone());
            acc
        })
        .into_iter()
        .map(|(file_path, hunks)| VirtualBranchFile {
            id: file_path.display().to_string(),
            path: file_path.clone(),
            hunks: hunks.clone(),
            binary: hunks.iter().any(|h| h.binary),
            large: false,
            modified_at: hunks.iter().map(|h| h.modified_at).max().unwrap_or(0),
            conflicted: conflicts::is_conflicting(
                project_repository,
                Some(&file_path.display().to_string()),
            )
            .unwrap_or(false),
        })
        .collect::<Vec<_>>()
}

// reset virtual branch to a specific commit
pub fn reset_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    target_commit_oid: git::Oid,
) -> Result<(), errors::ResetBranchError> {
    let current_session = gb_repository.get_or_create_current_session()?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)?;

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to read default target")?
        .ok_or_else(|| {
            errors::ResetBranchError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let mut branch = match branch_reader.read(branch_id) {
        Ok(branch) => Ok(branch),
        Err(reader::Error::NotFound) => Err(errors::ResetBranchError::BranchNotFound(
            errors::BranchNotFound {
                branch_id: *branch_id,
                project_id: project_repository.project().id,
            },
        )),
        Err(error) => Err(errors::ResetBranchError::Other(error.into())),
    }?;

    if branch.head == target_commit_oid {
        // nothing to do
        return Ok(());
    }

    if default_target.sha != target_commit_oid
        && !project_repository
            .l(branch.head, LogUntil::Commit(default_target.sha))?
            .contains(&target_commit_oid)
    {
        return Err(errors::ResetBranchError::CommitNotFoundInBranch(
            target_commit_oid,
        ));
    }

    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    branch.head = target_commit_oid;
    branch_writer
        .write(&mut branch)
        .context("failed to write branch")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)
        .context("failed to update gitbutler integration")?;

    Ok(())
}

fn diffs_to_virtual_files(
    project_repository: &project_repository::Repository,
    diffs: &HashMap<PathBuf, Vec<diff::GitHunk>>,
) -> Vec<VirtualBranchFile> {
    let hunks_by_filepath = virtual_hunks_by_filepath(&project_repository.project().path, diffs);
    virtual_hunks_to_virtual_files(
        project_repository,
        &hunks_by_filepath
            .values()
            .flatten()
            .cloned()
            .collect::<Vec<_>>(),
    )
}

// this function takes a list of file ownership,
// constructs a tree from those changes on top of the target
// and writes it as a new tree for storage
pub fn write_tree(
    project_repository: &project_repository::Repository,
    target: &git::Oid,
    files: &HashMap<PathBuf, Vec<diff::GitHunk>>,
) -> Result<git::Oid> {
    write_tree_onto_commit(project_repository, *target, files)
}

pub fn write_tree_onto_commit(
    project_repository: &project_repository::Repository,
    commit_oid: git::Oid,
    files: &HashMap<PathBuf, Vec<diff::GitHunk>>,
) -> Result<git::Oid> {
    // read the base sha into an index
    let git_repository = &project_repository.git_repository;

    let head_commit = git_repository.find_commit(commit_oid)?;
    let base_tree = head_commit.tree()?;

    write_tree_onto_tree(project_repository, &base_tree, files)
}

pub fn write_tree_onto_tree(
    project_repository: &project_repository::Repository,
    base_tree: &git::Tree,
    files: &HashMap<PathBuf, Vec<diff::GitHunk>>,
) -> Result<git::Oid> {
    let git_repository = &project_repository.git_repository;
    let mut builder = git_repository.treebuilder(Some(base_tree));
    // now update the index with content in the working directory for each file
    for (filepath, hunks) in files {
        // convert this string to a Path
        let rel_path = Path::new(&filepath);
        let full_path = project_repository.path().join(rel_path);

        let is_submodule =
            full_path.is_dir() && hunks.len() == 1 && hunks[0].diff.contains("Subproject commit");

        // if file exists
        if full_path.exists() {
            // if file is executable, use 755, otherwise 644
            let mut filemode = git::FileMode::Blob;
            // check if full_path file is executable
            if let Ok(metadata) = std::fs::symlink_metadata(&full_path) {
                #[cfg(target_family = "unix")]
                {
                    if metadata.permissions().mode() & 0o111 != 0 {
                        filemode = git::FileMode::BlobExecutable;
                    }
                }
                #[cfg(target_os = "windows")]
                {
                    // TODO(qix-): Pull from `core.filemode` config option to determine
                    // TODO(qix-): the behavior on windows. For now, we set this to true.
                    // TODO(qix-): It's not ideal, but it gets us to a windows build faster.
                    filemode = git::FileMode::BlobExecutable;
                }

                if metadata.file_type().is_symlink() {
                    filemode = git::FileMode::Link;
                }
            }

            // get the blob
            if filemode == git::FileMode::Link {
                // it's a symlink, make the content the path of the link
                let link_target = std::fs::read_link(&full_path)?;

                // if the link target is inside the project repository, make it relative
                let link_target = link_target
                    .strip_prefix(project_repository.path())
                    .unwrap_or(&link_target);

                let blob_oid = git_repository.blob(
                    link_target
                        .to_str()
                        .ok_or_else(|| {
                            anyhow!("path contains invalid utf-8 characters: {link_target:?}")
                        })?
                        .as_bytes(),
                )?;
                builder.upsert(rel_path, blob_oid, filemode);
            } else if let Ok(tree_entry) = base_tree.get_path(rel_path) {
                if hunks.len() == 1 && hunks[0].binary {
                    let new_blob_oid = &hunks[0].diff;
                    // convert string to Oid
                    let new_blob_oid = new_blob_oid.parse().context("failed to diff as oid")?;
                    builder.upsert(rel_path, new_blob_oid, filemode);
                } else {
                    // blob from tree_entry
                    let blob = tree_entry
                        .to_object(git_repository)
                        .unwrap()
                        .peel_to_blob()
                        .context("failed to get blob")?;

                    let mut blob_contents = blob.content().to_str()?.to_string();

                    let mut hunks = hunks.clone();
                    hunks.sort_by_key(|hunk| hunk.new_start);
                    let mut all_diffs = String::new();
                    for hunk in hunks {
                        all_diffs.push_str(&hunk.diff);
                    }

                    let patch = Patch::from_str(&all_diffs)?;
                    blob_contents = apply(&blob_contents, &patch).context(format!(
                        "failed to apply\n{}\nonto:\n{}",
                        &all_diffs, &blob_contents
                    ))?;

                    // create a blob
                    let new_blob_oid = git_repository.blob(blob_contents.as_bytes())?;
                    // upsert into the builder
                    builder.upsert(rel_path, new_blob_oid, filemode);
                }
            } else if is_submodule {
                let mut blob_contents = String::new();

                let mut hunks = hunks.clone();
                hunks.sort_by_key(|hunk| hunk.new_start);
                for hunk in hunks {
                    let patch = Patch::from_str(&hunk.diff)?;
                    blob_contents = apply(&blob_contents, &patch)
                        .context(format!("failed to apply {}", &hunk.diff))?;
                }

                // create a blob
                let new_blob_oid = git_repository.blob(blob_contents.as_bytes())?;
                // upsert into the builder
                builder.upsert(rel_path, new_blob_oid, filemode);
            } else {
                // create a git blob from a file on disk
                let blob_oid = git_repository
                    .blob_path(&full_path)
                    .context(format!("failed to create blob from path {:?}", &full_path))?;
                builder.upsert(rel_path, blob_oid, filemode);
            }
        } else if base_tree.get_path(rel_path).is_ok() {
            // remove file from index if it exists in the base tree
            builder.remove(rel_path);
        } else {
            // file not in index or base tree, do nothing
            // this is the
        }
    }

    // now write out the tree
    let tree_oid = builder.write().context("failed to write updated tree")?;

    Ok(tree_oid)
}

fn _print_tree(repo: &git2::Repository, tree: &git2::Tree) -> Result<()> {
    println!("tree id: {}", tree.id());
    for entry in tree {
        println!(
            "  entry: {} {}",
            entry.name().unwrap_or_default(),
            entry.id()
        );
        // get entry contents
        let object = entry.to_object(repo).context("failed to get object")?;
        let blob = object.as_blob().context("failed to get blob")?;
        // convert content to string
        if let Ok(content) = std::str::from_utf8(blob.content()) {
            println!("    blob: {}", content);
        } else {
            println!("    blob: BINARY");
        }
    }
    Ok(())
}

#[allow(clippy::too_many_arguments)]
pub fn commit(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    message: &str,
    ownership: Option<&branch::BranchOwnershipClaims>,
    signing_key: Option<&keys::PrivateKey>,
    user: Option<&users::User>,
    run_hooks: bool,
) -> Result<git::Oid, errors::CommitError> {
    let mut message_buffer = message.to_owned();

    if run_hooks {
        let hook_result = project_repository
            .git_repository
            .run_hook_commit_msg(&mut message_buffer)
            .context("failed to run hook")?;

        if let HookResult::RunNotSuccessful { stdout, .. } = hook_result {
            return Err(errors::CommitError::CommitMsgHookRejected(stdout));
        }

        let hook_result = project_repository
            .git_repository
            .run_hook_pre_commit()
            .context("failed to run hook")?;

        if let HookResult::RunNotSuccessful { stdout, .. } = hook_result {
            return Err(errors::CommitError::CommitHookRejected(stdout));
        }
    }

    let message = &message_buffer;

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;
    // get the files to commit
    let (mut statuses, _) =
        get_status_by_branch(gb_repository, project_repository, Some(&integration_commit))
            .context("failed to get status by branch")?;

    let (ref mut branch, files) = statuses
        .iter_mut()
        .find(|(branch, _)| branch.id == *branch_id)
        .ok_or_else(|| {
            errors::CommitError::BranchNotFound(errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            })
        })?;

    update_conflict_markers(project_repository, files)?;

    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::CommitError::Conflicted(errors::ProjectConflict {
            project_id: project_repository.project().id,
        }));
    }

    let tree_oid = if let Some(ownership) = ownership {
        let files = files
            .iter()
            .filter_map(|(filepath, hunks)| {
                let hunks = hunks
                    .iter()
                    .filter(|hunk| {
                        ownership
                            .claims
                            .iter()
                            .find(|f| f.file_path.eq(filepath))
                            .map_or(false, |f| {
                                f.hunks.iter().any(|h| {
                                    h.start == hunk.new_start
                                        && h.end == hunk.new_start + hunk.new_lines
                                })
                            })
                    })
                    .cloned()
                    .collect::<Vec<_>>();
                if hunks.is_empty() {
                    None
                } else {
                    Some((filepath.clone(), hunks))
                }
            })
            .collect::<HashMap<_, _>>();
        write_tree_onto_commit(project_repository, branch.head, &files)?
    } else {
        write_tree_onto_commit(project_repository, branch.head, files)?
    };

    let git_repository = &project_repository.git_repository;
    let parent_commit = git_repository
        .find_commit(branch.head)
        .context(format!("failed to find commit {:?}", branch.head))?;
    let tree = git_repository
        .find_tree(tree_oid)
        .context(format!("failed to find tree {:?}", tree_oid))?;

    // now write a commit, using a merge parent if it exists
    let extra_merge_parent =
        conflicts::merge_parent(project_repository).context("failed to get merge parent")?;

    let commit_oid = match extra_merge_parent {
        Some(merge_parent) => {
            let merge_parent = git_repository
                .find_commit(merge_parent)
                .context(format!("failed to find merge parent {:?}", merge_parent))?;
            let commit_oid = project_repository.commit(
                user,
                message,
                &tree,
                &[&parent_commit, &merge_parent],
                signing_key,
            )?;
            conflicts::clear(project_repository).context("failed to clear conflicts")?;
            commit_oid
        }
        None => project_repository.commit(user, message, &tree, &[&parent_commit], signing_key)?,
    };

    if run_hooks {
        project_repository
            .git_repository
            .run_hook_post_commit()
            .context("failed to run hook")?;
    }

    // update the virtual branch head
    let writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    branch.tree = tree_oid;
    branch.head = commit_oid;
    writer.write(branch).context("failed to write branch")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)
        .context("failed to update gitbutler integration")?;

    Ok(commit_oid)
}

pub fn push(
    project_repository: &project_repository::Repository,
    gb_repository: &gb_repository::Repository,
    branch_id: &BranchId,
    with_force: bool,
    credentials: &git::credentials::Helper,
    askpass: Option<(AskpassBroker, Option<BranchId>)>,
) -> Result<(), errors::PushError> {
    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create currnt session")
        .map_err(errors::PushError::Other)?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")
        .map_err(errors::PushError::Other)?;

    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;

    let mut vbranch = branch_reader.read(branch_id).map_err(|error| match error {
        reader::Error::NotFound => errors::PushError::BranchNotFound(errors::BranchNotFound {
            project_id: project_repository.project().id,
            branch_id: *branch_id,
        }),
        error => errors::PushError::Other(error.into()),
    })?;

    let remote_branch = if let Some(upstream_branch) = vbranch.upstream.as_ref() {
        upstream_branch.clone()
    } else {
        let default_target =
            get_default_target(&current_session_reader, project_repository.project())
                .context("failed to get default target")?
                .ok_or_else(|| {
                    errors::PushError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                        project_id: project_repository.project().id,
                    })
                })?;

        let remote_branch = format!(
            "refs/remotes/{}/{}",
            default_target.branch.remote(),
            normalize_branch_name(&vbranch.name)
        )
        .parse::<git::RemoteRefname>()
        .context("failed to parse remote branch name")?;

        let remote_branches = project_repository.git_remote_branches()?;
        let existing_branches = remote_branches
            .iter()
            .map(RemoteRefname::branch)
            .map(str::to_lowercase) // git is weird about case sensitivity here, assume not case sensitive
            .collect::<Vec<_>>();

        remote_branch.with_branch(&dedup_fmt(
            &existing_branches
                .iter()
                .map(String::as_str)
                .collect::<Vec<_>>(),
            remote_branch.branch(),
            "-",
        ))
    };

    project_repository.push(
        &vbranch.head,
        &remote_branch,
        with_force,
        credentials,
        None,
        askpass.clone(),
    )?;

    vbranch.upstream = Some(remote_branch.clone());
    vbranch.upstream_head = Some(vbranch.head);
    branch_writer
        .write(&mut vbranch)
        .context("failed to write target branch after push")?;
    project_repository.fetch(
        remote_branch.remote(),
        credentials,
        askpass.map(|(broker, _)| (broker, "modal".to_string())),
    )?;

    Ok(())
}

fn is_commit_integrated(
    project_repository: &project_repository::Repository,
    target: &target::Target,
    commit: &git::Commit,
) -> Result<bool> {
    let remote_branch = project_repository
        .git_repository
        .find_branch(&target.branch.clone().into())?;
    let remote_head = remote_branch.peel_to_commit()?;
    let upstream_commits = project_repository.l(
        remote_head.id(),
        project_repository::LogUntil::Commit(target.sha),
    )?;

    if target.sha.eq(&commit.id()) {
        // could not be integrated if heads are the same.
        return Ok(false);
    }

    if upstream_commits.is_empty() {
        // could not be integrated - there is nothing new upstream.
        return Ok(false);
    }

    if upstream_commits.contains(&commit.id()) {
        return Ok(true);
    }

    let merge_base_id = project_repository
        .git_repository
        .merge_base(target.sha, commit.id())?;
    if merge_base_id.eq(&commit.id()) {
        // if merge branch is the same as branch head and there are upstream commits
        // then it's integrated
        return Ok(true);
    }

    let merge_base = project_repository
        .git_repository
        .find_commit(merge_base_id)?;
    let merge_base_tree = merge_base.tree()?;
    let upstream = project_repository
        .git_repository
        .find_commit(remote_head.id())?;
    let upstream_tree = upstream.tree()?;

    if merge_base_tree.id() == upstream_tree.id() {
        // if merge base is the same as upstream tree, then it's integrated
        return Ok(true);
    }

    // try to merge our tree into the upstream tree
    let mut merge_index = project_repository
        .git_repository
        .merge_trees(&merge_base_tree, &commit.tree()?, &upstream_tree)
        .context("failed to merge trees")?;

    if merge_index.has_conflicts() {
        return Ok(false);
    }

    let merge_tree_oid = merge_index
        .write_tree_to(&project_repository.git_repository)
        .context("failed to write tree")?;

    // if the merge_tree is the same as the new_target_tree and there are no files (uncommitted changes)
    // then the vbranch is fully merged
    Ok(merge_tree_oid == upstream_tree.id())
}

pub fn is_remote_branch_mergeable(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_name: &git::RemoteRefname,
) -> Result<bool, errors::IsRemoteBranchMergableError> {
    // get the current target
    let latest_session = gb_repository.get_latest_session()?.ok_or_else(|| {
        errors::IsRemoteBranchMergableError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
            project_id: project_repository.project().id,
        })
    })?;
    let session_reader = sessions::Reader::open(gb_repository, &latest_session)
        .context("failed to open current session")?;

    let default_target = get_default_target(&session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::IsRemoteBranchMergableError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let target_commit = project_repository
        .git_repository
        .find_commit(default_target.sha)
        .context("failed to find target commit")?;

    let branch = match project_repository
        .git_repository
        .find_branch(&branch_name.into())
    {
        Ok(branch) => Ok(branch),
        Err(git::Error::NotFound(_)) => Err(errors::IsRemoteBranchMergableError::BranchNotFound(
            branch_name.clone(),
        )),
        Err(error) => Err(errors::IsRemoteBranchMergableError::Other(error.into())),
    }?;
    let branch_oid = branch.target().context("detatched head")?;
    let branch_commit = project_repository
        .git_repository
        .find_commit(branch_oid)
        .context("failed to find branch commit")?;

    let base_tree = find_base_tree(
        &project_repository.git_repository,
        &branch_commit,
        &target_commit,
    )?;

    let wd_tree = project_repository.get_wd_tree()?;

    let branch_tree = branch_commit.tree().context("failed to find branch tree")?;
    let mergeable = !project_repository
        .git_repository
        .merge_trees(&base_tree, &branch_tree, &wd_tree)
        .context("failed to merge trees")?
        .has_conflicts();

    Ok(mergeable)
}

pub fn is_virtual_branch_mergeable(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
) -> Result<bool, errors::IsVirtualBranchMergeable> {
    let latest_session = gb_repository.get_latest_session()?.ok_or_else(|| {
        errors::IsVirtualBranchMergeable::DefaultTargetNotSet(errors::DefaultTargetNotSet {
            project_id: project_repository.project().id,
        })
    })?;
    let session_reader = sessions::Reader::open(gb_repository, &latest_session)
        .context("failed to open current session reader")?;
    let branch_reader = branch::Reader::new(
        &session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let branch = match branch_reader.read(branch_id) {
        Ok(branch) => Ok(branch),
        Err(reader::Error::NotFound) => Err(errors::IsVirtualBranchMergeable::BranchNotFound(
            errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            },
        )),
        Err(error) => Err(errors::IsVirtualBranchMergeable::Other(error.into())),
    }?;

    if branch.applied {
        return Ok(true);
    }

    let default_target = get_default_target(&session_reader, project_repository.project())
        .context("failed to read default target")?
        .ok_or_else(|| {
            errors::IsVirtualBranchMergeable::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    // determine if this branch is up to date with the target/base
    let merge_base = project_repository
        .git_repository
        .merge_base(default_target.sha, branch.head)
        .context("failed to find merge base")?;

    if merge_base != default_target.sha {
        return Ok(false);
    }

    let branch_commit = project_repository
        .git_repository
        .find_commit(branch.head)
        .context("failed to find branch commit")?;

    let target_commit = project_repository
        .git_repository
        .find_commit(default_target.sha)
        .context("failed to find target commit")?;

    let base_tree = find_base_tree(
        &project_repository.git_repository,
        &branch_commit,
        &target_commit,
    )?;

    let wd_tree = project_repository.get_wd_tree()?;

    // determine if this tree is mergeable
    let branch_tree = project_repository
        .git_repository
        .find_tree(branch.tree)
        .context("failed to find branch tree")?;

    let is_mergeable = !project_repository
        .git_repository
        .merge_trees(&base_tree, &branch_tree, &wd_tree)
        .context("failed to merge trees")?
        .has_conflicts();

    Ok(is_mergeable)
}

pub fn amend(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    target_ownership: &BranchOwnershipClaims,
) -> Result<git::Oid, errors::AmendError> {
    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::AmendError::Conflict(errors::ProjectConflict {
            project_id: project_repository.project().id,
        }));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;

    let all_branches = Iterator::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .collect::<Vec<_>>();

    if !all_branches.iter().any(|b| b.id == *branch_id) {
        return Err(errors::AmendError::BranchNotFound(errors::BranchNotFound {
            project_id: project_repository.project().id,
            branch_id: *branch_id,
        }));
    }

    let applied_branches = all_branches
        .into_iter()
        .filter(|b| b.applied)
        .collect::<Vec<_>>();

    if !applied_branches.iter().any(|b| b.id == *branch_id) {
        return Err(errors::AmendError::BranchNotFound(errors::BranchNotFound {
            project_id: project_repository.project().id,
            branch_id: *branch_id,
        }));
    }

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to read default target")?
        .ok_or_else(|| {
            errors::AmendError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    let (mut applied_statuses, _) = get_applied_status(
        gb_repository,
        project_repository,
        &integration_commit,
        &default_target.sha,
        applied_branches,
    )?;

    let (ref mut target_branch, target_status) = applied_statuses
        .iter_mut()
        .find(|(b, _)| b.id == *branch_id)
        .ok_or_else(|| {
            errors::AmendError::BranchNotFound(errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            })
        })?;

    if target_branch.upstream.is_some() && !project_repository.project().ok_with_force_push {
        // amending to a pushed head commit will cause a force push that is not allowed
        return Err(errors::AmendError::ForcePushNotAllowed(
            errors::ForcePushNotAllowed {
                project_id: project_repository.project().id,
            },
        ));
    }

    if project_repository
        .l(
            target_branch.head,
            project_repository::LogUntil::Commit(default_target.sha),
        )?
        .is_empty()
    {
        return Err(errors::AmendError::BranchHasNoCommits);
    }

    let head_commit = project_repository
        .git_repository
        .find_commit(target_branch.head)
        .context("failed to find head commit")?;

    let diffs_to_amend = target_ownership
        .claims
        .iter()
        .filter_map(|file_ownership| {
            let hunks = target_status
                .get(&file_ownership.file_path)
                .map(|hunks| {
                    hunks
                        .iter()
                        .filter(|hunk| {
                            file_ownership.hunks.iter().any(|owned_hunk| {
                                owned_hunk.start == hunk.new_start
                                    && owned_hunk.end == hunk.new_start + hunk.new_lines
                            })
                        })
                        .cloned()
                        .collect::<Vec<_>>()
                })
                .unwrap_or_default();
            if hunks.is_empty() {
                None
            } else {
                Some((file_ownership.file_path.clone(), hunks))
            }
        })
        .collect::<HashMap<_, _>>();

    if diffs_to_amend.is_empty() {
        return Err(errors::AmendError::TargetOwnerhshipNotFound(
            target_ownership.clone(),
        ));
    }

    let new_tree_oid =
        write_tree_onto_commit(project_repository, target_branch.head, &diffs_to_amend)?;
    let new_tree = project_repository
        .git_repository
        .find_tree(new_tree_oid)
        .context("failed to find new tree")?;

    let parents = head_commit
        .parents()
        .context("failed to find head commit parents")?;

    let commit_oid = project_repository
        .git_repository
        .commit(
            None,
            &head_commit.author(),
            &head_commit.committer(),
            head_commit.message().unwrap_or_default(),
            &new_tree,
            &parents.iter().collect::<Vec<_>>(),
        )
        .context("failed to create commit")?;

    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    target_branch.head = commit_oid;
    branch_writer.write(target_branch)?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(commit_oid)
}

pub fn cherry_pick(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    target_commit_oid: git::Oid,
) -> Result<Option<git::Oid>, errors::CherryPickError> {
    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::CherryPickError::Conflict(errors::ProjectConflict {
            project_id: project_repository.project().id,
        }));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );
    let mut branch = branch_reader
        .read(branch_id)
        .context("failed to read branch")?;

    if !branch.applied {
        // todo?
        return Err(errors::CherryPickError::NotApplied);
    }

    let target_commit = project_repository
        .git_repository
        .find_commit(target_commit_oid)
        .map_err(|error| match error {
            git::Error::NotFound(_) => errors::CherryPickError::CommitNotFound(target_commit_oid),
            error => errors::CherryPickError::Other(error.into()),
        })?;

    let branch_head_commit = project_repository
        .git_repository
        .find_commit(branch.head)
        .context("failed to find branch tree")?;

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to read default target")?
        .context("no default target set")?;

    // if any other branches are applied, unapply them
    let applied_branches = Iterator::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .filter(|b| b.applied)
    .collect::<Vec<_>>();

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    let (applied_statuses, _) = get_applied_status(
        gb_repository,
        project_repository,
        &integration_commit,
        &default_target.sha,
        applied_branches,
    )?;

    let branch_files = applied_statuses
        .iter()
        .find(|(b, _)| b.id == *branch_id)
        .map(|(_, f)| f)
        .context("branch status not found")?;

    // create a wip commit. we'll use it to offload cherrypick conflicts calculation to libgit.
    let wip_commit = {
        let wip_tree_oid = write_tree(project_repository, &branch.head, branch_files)?;
        let wip_tree = project_repository
            .git_repository
            .find_tree(wip_tree_oid)
            .context("failed to find tree")?;

        let signature = git::Signature::now("GitButler", "gitbutler@gitbutler.com")
            .context("failed to make gb signature")?;
        let oid = project_repository
            .git_repository
            .commit(
                None,
                &signature,
                &signature,
                "wip cherry picking commit",
                &wip_tree,
                &[&branch_head_commit],
            )
            .context("failed to commit wip work")?;
        project_repository
            .git_repository
            .find_commit(oid)
            .context("failed to find wip commit")?
    };

    let mut cherrypick_index = project_repository
        .git_repository
        .cherry_pick(&wip_commit, &target_commit)
        .context("failed to cherry pick")?;

    // unapply other branches
    for other_branch in applied_statuses
        .iter()
        .filter(|(b, _)| b.id != branch.id)
        .map(|(b, _)| b)
    {
        unapply_branch(gb_repository, project_repository, &other_branch.id)
            .context("failed to unapply branch")?;
    }

    let commit_oid = if cherrypick_index.has_conflicts() {
        // checkout the conflicts
        project_repository
            .git_repository
            .checkout_index(&mut cherrypick_index)
            .allow_conflicts()
            .conflict_style_merge()
            .force()
            .checkout()
            .context("failed to checkout conflicts")?;

        // mark conflicts
        let conflicts = cherrypick_index
            .conflicts()
            .context("failed to get conflicts")?;
        let mut merge_conflicts = Vec::new();
        for path in conflicts.flatten() {
            if let Some(ours) = path.our {
                let path = std::str::from_utf8(&ours.path)
                    .context("failed to convert path")?
                    .to_string();
                merge_conflicts.push(path);
            }
        }
        conflicts::mark(project_repository, &merge_conflicts, Some(branch.head))?;

        None
    } else {
        let merge_tree_oid = cherrypick_index
            .write_tree_to(&project_repository.git_repository)
            .context("failed to write merge tree")?;
        let merge_tree = project_repository
            .git_repository
            .find_tree(merge_tree_oid)
            .context("failed to find merge tree")?;

        let branch_head_commit = project_repository
            .git_repository
            .find_commit(branch.head)
            .context("failed to find branch head commit")?;

        let commit_oid = project_repository
            .git_repository
            .commit(
                None,
                &target_commit.author(),
                &target_commit.committer(),
                target_commit.message().unwrap_or_default(),
                &merge_tree,
                &[&branch_head_commit],
            )
            .context("failed to create commit")?;

        // checkout final_tree into the working directory
        project_repository
            .git_repository
            .checkout_tree(&merge_tree)
            .force()
            .remove_untracked()
            .checkout()
            .context("failed to checkout final tree")?;

        // update branch status
        let writer = branch::Writer::new(
            gb_repository,
            VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        )
        .context("failed to create writer")?;
        branch.head = commit_oid;
        writer
            .write(&mut branch)
            .context("failed to write branch")?;

        Some(commit_oid)
    };

    super::integration::update_gitbutler_integration(gb_repository, project_repository)
        .context("failed to update gitbutler integration")?;

    Ok(commit_oid)
}

/// squashes a commit from a virtual branch into it's parent.
pub fn squash(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    commit_oid: git::Oid,
) -> Result<(), errors::SquashError> {
    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::SquashError::Conflict(errors::ProjectConflict {
            project_id: project_repository.project().id,
        }));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to read default target")?
        .ok_or_else(|| {
            errors::SquashError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let mut branch = branch_reader.read(branch_id).map_err(|error| match error {
        reader::Error::NotFound => errors::SquashError::BranchNotFound(errors::BranchNotFound {
            project_id: project_repository.project().id,
            branch_id: *branch_id,
        }),
        error => errors::SquashError::Other(error.into()),
    })?;

    let branch_commit_oids = project_repository.l(
        branch.head,
        project_repository::LogUntil::Commit(default_target.sha),
    )?;

    if !branch_commit_oids.contains(&commit_oid) {
        return Err(errors::SquashError::CommitNotFound(commit_oid));
    }

    let commit_to_squash = project_repository
        .git_repository
        .find_commit(commit_oid)
        .context("failed to find commit")?;

    let parent_commit = commit_to_squash
        .parent(0)
        .context("failed to find parent commit")?;

    let pushed_commit_oids = branch.upstream_head.map_or_else(
        || Ok(vec![]),
        |upstream_head| {
            project_repository.l(
                upstream_head,
                project_repository::LogUntil::Commit(default_target.sha),
            )
        },
    )?;

    if pushed_commit_oids.contains(&parent_commit.id())
        && !project_repository.project().ok_with_force_push
    {
        // squashing into a pushed commit will cause a force push that is not allowed
        return Err(errors::SquashError::ForcePushNotAllowed(
            errors::ForcePushNotAllowed {
                project_id: project_repository.project().id,
            },
        ));
    }

    if !branch_commit_oids.contains(&parent_commit.id()) {
        return Err(errors::SquashError::CantSquashRootCommit);
    }

    let ids_to_rebase = {
        let ids = branch_commit_oids
            .split(|oid| oid.eq(&commit_oid))
            .collect::<Vec<_>>();
        ids.first().copied()
    };

    // create a commit that:
    //  * has the tree of the target commit
    //  * has the message combined of the target commit and parent commit
    //  * has parents of the parents commit.
    let parents = parent_commit
        .parents()
        .context("failed to find head commit parents")?;

    let new_commit_oid = project_repository
        .git_repository
        .commit(
            None,
            &commit_to_squash.author(),
            &commit_to_squash.committer(),
            &format!(
                "{}\n{}",
                parent_commit.message().unwrap_or_default(),
                commit_to_squash.message().unwrap_or_default(),
            ),
            &commit_to_squash.tree().context("failed to find tree")?,
            &parents.iter().collect::<Vec<_>>(),
        )
        .context("failed to commit")?;

    let new_head_id = if let Some(ids_to_rebase) = ids_to_rebase {
        let mut ids_to_rebase = ids_to_rebase.to_vec();
        ids_to_rebase.reverse();

        // now, rebase unchanged commits onto the new commit
        let commits_to_rebase = ids_to_rebase
            .iter()
            .map(|oid| project_repository.git_repository.find_commit(*oid))
            .collect::<Result<Vec<_>, _>>()
            .context("failed to read commits to rebase")?;

        commits_to_rebase
            .into_iter()
            .fold(
                project_repository
                    .git_repository
                    .find_commit(new_commit_oid)
                    .context("failed to find new commit"),
                |head, to_rebase| {
                    let head = head?;

                    let mut cherrypick_index = project_repository
                        .git_repository
                        .cherry_pick(&head, &to_rebase)
                        .context("failed to cherry pick")?;

                    if cherrypick_index.has_conflicts() {
                        bail!("failed to rebase");
                    }

                    let merge_tree_oid = cherrypick_index
                        .write_tree_to(&project_repository.git_repository)
                        .context("failed to write merge tree")?;

                    let merge_tree = project_repository
                        .git_repository
                        .find_tree(merge_tree_oid)
                        .context("failed to find merge tree")?;

                    let commit_oid = project_repository
                        .git_repository
                        .commit(
                            None,
                            &to_rebase.author(),
                            &to_rebase.committer(),
                            to_rebase.message().unwrap_or_default(),
                            &merge_tree,
                            &[&head],
                        )
                        .context("failed to create commit")?;

                    project_repository
                        .git_repository
                        .find_commit(commit_oid)
                        .context("failed to find commit")
                },
            )?
            .id()
    } else {
        new_commit_oid
    };

    // save new branch head
    let writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    branch.head = new_head_id;
    writer
        .write(&mut branch)
        .context("failed to write branch")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(())
}

pub fn update_commit_message(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    branch_id: &BranchId,
    commit_oid: git::Oid,
    message: &str,
) -> Result<(), errors::UpdateCommitMessageError> {
    if message.is_empty() {
        return Err(errors::UpdateCommitMessageError::EmptyMessage);
    }

    if conflicts::is_conflicting::<&Path>(project_repository, None)? {
        return Err(errors::UpdateCommitMessageError::Conflict(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;
    let branch_reader = branch::Reader::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to read default target")?
        .ok_or_else(|| {
            errors::UpdateCommitMessageError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let mut branch = branch_reader.read(branch_id).map_err(|error| match error {
        reader::Error::NotFound => {
            errors::UpdateCommitMessageError::BranchNotFound(errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *branch_id,
            })
        }
        error => errors::UpdateCommitMessageError::Other(error.into()),
    })?;

    let branch_commit_oids = project_repository.l(
        branch.head,
        project_repository::LogUntil::Commit(default_target.sha),
    )?;

    if !branch_commit_oids.contains(&commit_oid) {
        return Err(errors::UpdateCommitMessageError::CommitNotFound(commit_oid));
    }

    let pushed_commit_oids = branch.upstream_head.map_or_else(
        || Ok(vec![]),
        |upstream_head| {
            project_repository.l(
                upstream_head,
                project_repository::LogUntil::Commit(default_target.sha),
            )
        },
    )?;

    if pushed_commit_oids.contains(&commit_oid) && !project_repository.project().ok_with_force_push
    {
        // updating the message of a pushed commit will cause a force push that is not allowed
        return Err(errors::UpdateCommitMessageError::ForcePushNotAllowed(
            errors::ForcePushNotAllowed {
                project_id: project_repository.project().id,
            },
        ));
    }

    let target_commit = project_repository
        .git_repository
        .find_commit(commit_oid)
        .context("failed to find commit")?;

    let ids_to_rebase = {
        let ids = branch_commit_oids
            .split(|oid| oid.eq(&commit_oid))
            .collect::<Vec<_>>();
        ids.first().copied()
    };

    let parents = target_commit
        .parents()
        .context("failed to find head commit parents")?;

    let new_commit_oid = project_repository
        .git_repository
        .commit(
            None,
            &target_commit.author(),
            &target_commit.committer(),
            message,
            &target_commit.tree().context("failed to find tree")?,
            &parents.iter().collect::<Vec<_>>(),
        )
        .context("failed to commit")?;

    let new_head_id = if let Some(ids_to_rebase) = ids_to_rebase {
        let mut ids_to_rebase = ids_to_rebase.to_vec();
        ids_to_rebase.reverse();
        // now, rebase unchanged commits onto the new commit
        let commits_to_rebase = ids_to_rebase
            .iter()
            .map(|oid| project_repository.git_repository.find_commit(*oid))
            .collect::<Result<Vec<_>, _>>()
            .context("failed to read commits to rebase")?;

        commits_to_rebase
            .into_iter()
            .fold(
                project_repository
                    .git_repository
                    .find_commit(new_commit_oid)
                    .context("failed to find new commit"),
                |head, to_rebase| {
                    let head = head?;

                    let mut cherrypick_index = project_repository
                        .git_repository
                        .cherry_pick(&head, &to_rebase)
                        .context("failed to cherry pick")?;

                    if cherrypick_index.has_conflicts() {
                        bail!("failed to rebase");
                    }

                    let merge_tree_oid = cherrypick_index
                        .write_tree_to(&project_repository.git_repository)
                        .context("failed to write merge tree")?;

                    let merge_tree = project_repository
                        .git_repository
                        .find_tree(merge_tree_oid)
                        .context("failed to find merge tree")?;

                    let commit_oid = project_repository
                        .git_repository
                        .commit(
                            None,
                            &to_rebase.author(),
                            &to_rebase.committer(),
                            to_rebase.message().unwrap_or_default(),
                            &merge_tree,
                            &[&head],
                        )
                        .context("failed to create commit")?;

                    project_repository
                        .git_repository
                        .find_commit(commit_oid)
                        .context("failed to find commit")
                },
            )?
            .id()
    } else {
        new_commit_oid
    };

    // save new branch head
    let writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    branch.head = new_head_id;
    writer
        .write(&mut branch)
        .context("failed to write branch")?;

    super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    Ok(())
}

/// moves commit on top of the to target branch
pub fn move_commit(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    target_branch_id: &BranchId,
    commit_oid: git::Oid,
    user: Option<&users::User>,
    signing_key: Option<&keys::PrivateKey>,
) -> Result<(), errors::MoveCommitError> {
    if project_repository.is_resolving() {
        return Err(errors::MoveCommitError::Conflicted(
            errors::ProjectConflict {
                project_id: project_repository.project().id,
            },
        ));
    }

    let latest_session = gb_repository
        .get_latest_session()
        .context("failed to get or create current session")?
        .ok_or_else(|| {
            errors::MoveCommitError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;
    let latest_session_reader = sessions::Reader::open(gb_repository, &latest_session)
        .context("failed to open current session")?;

    let applied_branches = Iterator::new(
        &latest_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .filter(|b| b.applied)
    .collect::<Vec<_>>();

    if !applied_branches.iter().any(|b| b.id == *target_branch_id) {
        return Err(errors::MoveCommitError::BranchNotFound(
            errors::BranchNotFound {
                project_id: project_repository.project().id,
                branch_id: *target_branch_id,
            },
        ));
    }

    let default_target = get_default_target(&latest_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::MoveCommitError::DefaultTargetNotSet(errors::DefaultTargetNotSet {
                project_id: project_repository.project().id,
            })
        })?;

    let integration_commit =
        super::integration::update_gitbutler_integration(gb_repository, project_repository)?;

    let (mut applied_statuses, _) = get_applied_status(
        gb_repository,
        project_repository,
        &integration_commit,
        &default_target.sha,
        applied_branches,
    )?;

    let (ref mut source_branch, source_status) = applied_statuses
        .iter_mut()
        .find(|(b, _)| b.head == commit_oid)
        .ok_or_else(|| errors::MoveCommitError::CommitNotFound(commit_oid))?;

    let source_branch_non_comitted_files = source_status;

    let source_branch_head = project_repository
        .git_repository
        .find_commit(commit_oid)
        .context("failed to find commit")?;
    let source_branch_head_parent = source_branch_head
        .parent(0)
        .context("failed to get parent commit")?;
    let source_branch_head_tree = source_branch_head
        .tree()
        .context("failed to get commit tree")?;
    let source_branch_head_parent_tree = source_branch_head_parent
        .tree()
        .context("failed to get parent tree")?;
    let branch_head_diff = diff::trees(
        &project_repository.git_repository,
        &source_branch_head_parent_tree,
        &source_branch_head_tree,
        context_lines(project_repository),
    )?;
    let branch_head_diff = diff::diff_files_to_hunks(&branch_head_diff);

    let is_source_locked = source_branch_non_comitted_files
        .iter()
        .any(|(path, hunks)| {
            branch_head_diff.get(path).map_or(false, |head_diff_hunks| {
                hunks.iter().any(|hunk| {
                    head_diff_hunks.iter().any(|head_hunk| {
                        joined(
                            head_hunk.new_start,
                            head_hunk.new_start + head_hunk.new_lines,
                            hunk.new_start,
                            hunk.new_start + hunk.new_lines,
                        )
                    })
                })
            })
        });

    if is_source_locked {
        return Err(errors::MoveCommitError::SourceLocked);
    }

    let branch_writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    let branch_reader = branch::Reader::new(
        &latest_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    );

    // move files ownerships from source branch to the destination branch

    let ownerships_to_transfer = branch_head_diff
        .iter()
        .map(|(file_path, hunks)| {
            (
                file_path.clone(),
                hunks.iter().map(Into::into).collect::<Vec<_>>(),
            )
        })
        .map(|(file_path, hunks)| OwnershipClaim { file_path, hunks })
        .flat_map(|file_ownership| source_branch.ownership.take(&file_ownership))
        .collect::<Vec<_>>();

    // reset the source branch to the parent commit
    {
        source_branch.head = source_branch_head_parent.id();
        branch_writer.write(source_branch)?;
    }

    // move the commit to destination branch target branch
    {
        let mut destination_branch =
            branch_reader
                .read(target_branch_id)
                .map_err(|error| match error {
                    reader::Error::NotFound => {
                        errors::MoveCommitError::BranchNotFound(errors::BranchNotFound {
                            project_id: project_repository.project().id,
                            branch_id: *target_branch_id,
                        })
                    }
                    error => errors::MoveCommitError::Other(error.into()),
                })?;

        for ownership in ownerships_to_transfer {
            destination_branch.ownership.put(&ownership);
        }

        let new_destination_tree_oid = write_tree_onto_commit(
            project_repository,
            destination_branch.head,
            &branch_head_diff,
        )
        .context("failed to write tree onto commit")?;
        let new_destination_tree = project_repository
            .git_repository
            .find_tree(new_destination_tree_oid)
            .context("failed to find tree")?;

        let new_destination_head_oid = project_repository
            .commit(
                user,
                source_branch_head.message().unwrap_or_default(),
                &new_destination_tree,
                &[&project_repository
                    .git_repository
                    .find_commit(destination_branch.head)
                    .context("failed to get dst branch head commit")?],
                signing_key,
            )
            .context("failed to commit")?;

        destination_branch.head = new_destination_head_oid;
        branch_writer.write(&mut destination_branch)?;
    }

    super::integration::update_gitbutler_integration(gb_repository, project_repository)
        .context("failed to update gitbutler integration")?;

    Ok(())
}

pub fn create_virtual_branch_from_branch(
    gb_repository: &gb_repository::Repository,
    project_repository: &project_repository::Repository,
    upstream: &git::Refname,
    signing_key: Option<&keys::PrivateKey>,
    user: Option<&users::User>,
) -> Result<BranchId, errors::CreateVirtualBranchFromBranchError> {
    if !matches!(upstream, git::Refname::Local(_) | git::Refname::Remote(_)) {
        return Err(errors::CreateVirtualBranchFromBranchError::BranchNotFound(
            upstream.clone(),
        ));
    }

    let current_session = gb_repository
        .get_or_create_current_session()
        .context("failed to get or create current session")?;
    let current_session_reader = sessions::Reader::open(gb_repository, &current_session)
        .context("failed to open current session")?;

    let default_target = get_default_target(&current_session_reader, project_repository.project())
        .context("failed to get default target")?
        .ok_or_else(|| {
            errors::CreateVirtualBranchFromBranchError::DefaultTargetNotSet(
                errors::DefaultTargetNotSet {
                    project_id: project_repository.project().id,
                },
            )
        })?;

    if let git::Refname::Remote(remote_upstream) = upstream {
        if default_target.branch.eq(remote_upstream) {
            return Err(
                errors::CreateVirtualBranchFromBranchError::CantMakeBranchFromDefaultTarget,
            );
        }
    }

    let repo = &project_repository.git_repository;
    let head_reference = match repo.find_reference(upstream) {
        Ok(head) => Ok(head),
        Err(git::Error::NotFound(_)) => Err(
            errors::CreateVirtualBranchFromBranchError::BranchNotFound(upstream.clone()),
        ),
        Err(error) => Err(errors::CreateVirtualBranchFromBranchError::Other(
            error.into(),
        )),
    }?;
    let head_commit = head_reference
        .peel_to_commit()
        .context("failed to peel to commit")?;
    let head_commit_tree = head_commit.tree().context("failed to find tree")?;

    let all_virtual_branches = Iterator::new(
        &current_session_reader,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
        project_repository.project().use_toml_vbranches_state(),
    )
    .context("failed to create branch iterator")?
    .collect::<Result<Vec<branch::Branch>, reader::Error>>()
    .context("failed to read virtual branches")?
    .into_iter()
    .collect::<Vec<branch::Branch>>();

    let order = all_virtual_branches.len();

    let selected_for_changes = (!all_virtual_branches
        .iter()
        .any(|b| b.selected_for_changes.is_some()))
    .then_some(chrono::Utc::now().timestamp_millis());

    let now = time::UNIX_EPOCH
        .elapsed()
        .context("failed to get elapsed time")?
        .as_millis();

    // only set upstream if it's not the default target
    let upstream_branch = match upstream {
        git::Refname::Other(_) | git::Refname::Virtual(_) => {
            // we only support local or remote branches
            return Err(errors::CreateVirtualBranchFromBranchError::BranchNotFound(
                upstream.clone(),
            ));
        }
        git::Refname::Remote(remote) => Some(remote.clone()),
        git::Refname::Local(local) => local.remote().cloned(),
    };

    // add file ownership based off the diff
    let target_commit = repo
        .find_commit(default_target.sha)
        .map_err(|error| errors::CreateVirtualBranchFromBranchError::Other(error.into()))?;
    let merge_base_oid = repo
        .merge_base(target_commit.id(), head_commit.id())
        .map_err(|error| errors::CreateVirtualBranchFromBranchError::Other(error.into()))?;
    let merge_base_tree = repo
        .find_commit(merge_base_oid)
        .map_err(|error| errors::CreateVirtualBranchFromBranchError::Other(error.into()))?
        .tree()
        .map_err(|error| errors::CreateVirtualBranchFromBranchError::Other(error.into()))?;

    // do a diff between the head of this branch and the target base
    let diff = diff::trees(
        &project_repository.git_repository,
        &merge_base_tree,
        &head_commit_tree,
        context_lines(project_repository),
    )
    .context("failed to diff trees")?;
    let diff = diff::diff_files_to_hunks(&diff);

    let hunks_by_filepath =
        super::virtual_hunks_by_filepath(&project_repository.project().path, &diff);

    // assign ownership to the branch
    let ownership = hunks_by_filepath.values().flatten().fold(
        branch::BranchOwnershipClaims::default(),
        |mut ownership, hunk| {
            ownership.put(
                &format!("{}:{}", hunk.file_path.display(), hunk.id)
                    .parse()
                    .unwrap(),
            );
            ownership
        },
    );

    let mut branch = branch::Branch {
        id: BranchId::generate(),
        name: upstream
            .branch()
            .expect("always a branch reference")
            .to_string(),
        notes: String::new(),
        applied: false,
        upstream_head: upstream_branch.is_some().then_some(head_commit.id()),
        upstream: upstream_branch,
        tree: head_commit_tree.id(),
        head: head_commit.id(),
        created_timestamp_ms: now,
        updated_timestamp_ms: now,
        ownership,
        order,
        selected_for_changes,
    };

    let writer = branch::Writer::new(
        gb_repository,
        VirtualBranchesHandle::new(&project_repository.project().gb_dir()),
    )
    .context("failed to create writer")?;
    writer
        .write(&mut branch)
        .context("failed to write branch")?;

    project_repository.add_branch_reference(&branch)?;

    match apply_branch(
        gb_repository,
        project_repository,
        &branch.id,
        signing_key,
        user,
    ) {
        Ok(()) => Ok(branch.id),
        Err(errors::ApplyBranchError::BranchConflicts(_)) => {
            // if branch conflicts with the workspace, it's ok. keep it unapplied
            Ok(branch.id)
        }
        Err(error) => Err(errors::CreateVirtualBranchFromBranchError::ApplyBranch(
            error,
        )),
    }
}

pub fn context_lines(project_repository: &project_repository::Repository) -> u32 {
    let use_context = project_repository
        .project()
        .use_diff_context
        .unwrap_or(false);

    if use_context {
        3_u32
    } else {
        0_u32
    }
}

/// Just like [`diffy::apply()`], but on error it will attach hashes of the input `base_image` and `patch`.
pub fn apply(base_image: &str, patch: &Patch<'_, str>) -> Result<String> {
    fn md5_hash_hex(b: impl AsRef<[u8]>) -> String {
        format!("{:x}", md5::compute(b))
    }

    #[derive(Debug)]
    #[allow(dead_code)] // Read by Debug auto-impl, which doesn't count
    pub enum DebugLine {
        // Note that each of these strings is a hash only
        Context(String),
        Delete(String),
        Insert(String),
    }

    impl<'a> From<&diffy::Line<'a, str>> for DebugLine {
        fn from(line: &Line<'a, str>) -> Self {
            match line {
                Line::Context(s) => DebugLine::Context(md5_hash_hex(s)),
                Line::Delete(s) => DebugLine::Delete(md5_hash_hex(s)),
                Line::Insert(s) => DebugLine::Insert(md5_hash_hex(s)),
            }
        }
    }

    #[derive(Debug)]
    #[allow(dead_code)] // Read by Debug auto-impl, which doesn't count
    struct DebugHunk {
        old_range: diffy::HunkRange,
        new_range: diffy::HunkRange,
        lines: Vec<DebugLine>,
    }

    impl<'a> From<&diffy::Hunk<'a, str>> for DebugHunk {
        fn from(hunk: &diffy::Hunk<'a, str>) -> Self {
            Self {
                old_range: hunk.old_range(),
                new_range: hunk.new_range(),
                lines: hunk.lines().iter().map(Into::into).collect(),
            }
        }
    }

    #[derive(Debug)]
    #[allow(dead_code)] // Read by Debug auto-impl, which doesn't count
    struct DebugContext {
        base_image_hash: String,
        hunks: Vec<DebugHunk>,
    }

    impl std::fmt::Display for DebugContext {
        fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
            std::fmt::Debug::fmt(self, f)
        }
    }

    diffy_apply(base_image, patch).with_context(|| DebugContext {
        base_image_hash: md5_hash_hex(base_image),
        hunks: patch.hunks().iter().map(Into::into).collect(),
    })
}

#[cfg(test)]
mod tests {
    use super::*;
    #[test]
    fn joined_test() {
        assert!(!joined(1, 2, 3, 4));
        assert!(joined(1, 4, 2, 3));
        assert!(joined(2, 3, 1, 4));
        assert!(!joined(3, 4, 1, 2));

        assert!(joined(1, 2, 2, 3));
        assert!(joined(1, 3, 2, 3));
        assert!(joined(2, 3, 1, 2));

        assert!(!joined(1, 1, 2, 2));
        assert!(joined(1, 1, 1, 1));
        assert!(joined(1, 1, 1, 2));
        assert!(joined(1, 2, 2, 2));
    }

    #[test]
    fn normalize_branch_name_test() {
        assert_eq!(normalize_branch_name("feature/branch"), "feature/branch");
        assert_eq!(normalize_branch_name("foo#branch"), "foo#branch");
        assert_eq!(normalize_branch_name("foo!branch"), "foo-branch");
    }
}

// Goes through a set of changes and checks if conflicts are present. If no conflicts
// are present in a file it will be resolved, meaning it will be removed from the
// conflicts file.
fn update_conflict_markers(
    project_repository: &project_repository::Repository,
    files: &HashMap<PathBuf, Vec<GitHunk>>,
) -> Result<()> {
    let conflicting_files = conflicts::conflicting_files(project_repository)?;
    for (file_path, non_commited_hunks) in files {
        let mut conflicted = false;
        if conflicting_files.contains(&file_path.display().to_string()) {
            // check file for conflict markers, resolve the file if there are none in any hunk
            for hunk in non_commited_hunks {
                if hunk.diff.contains("<<<<<<< ours") {
                    conflicted = true;
                }
                if hunk.diff.contains(">>>>>>> theirs") {
                    conflicted = true;
                }
            }
            if !conflicted {
                conflicts::resolve(project_repository, &file_path.display().to_string()).unwrap();
            }
        }
    }
    Ok(())
}