orch/cli/

doctor.rs

use crate::backends::github::GitHubBackend;
use crate::backends::{ExternalBackend, ExternalId};
use crate::config;
use crate::engine::cleanup::{
    cleanup_orphaned_worktree, remove_worktree_and_branch, resolve_repo_root,
};
use crate::github::http::GhHttp;
use crate::store::{Task, TaskStatus, TaskStore};
use crate::tmux::TmuxManager;
use std::io::Write;
use std::path::Path;
use std::sync::Arc;
use std::sync::atomic::{AtomicBool, Ordering};

/// What kind of automatic repair can be applied to a finding.
///
/// Nothing here moves a done task out of done. Done is terminal, so a done task
/// that looks wrong is reported and left alone (#3780)
enum FixAction {
    /// PR exists but pr_number not recorded — link it in the store.
    LinkPr { store_id: i64, pr_number: u64 },
    /// GitHub issue is closed but task is not done — reopen issue, sync labels.
    ReopenIssue { store_id: i64 },
    /// Task is done but GitHub issue still open — close issue.
    CloseIssue { store_id: i64 },
    /// GitHub label doesn't match SQLite status — sync labels.
    SyncLabels { store_id: i64 },
    /// Stale in_progress — no tmux session — reset to routed.
    ResetToRouted { store_id: i64 },
    /// Done task with uncleaned worktree that has no uncommitted/unpushed work.
    CleanWorktree { store_id: i64 },
    /// Orphaned worktree with no owning task — remove directory.
    RemoveOrphanedWorktree { path: String },
    /// PR merged but task not done — set done, close issue, clean worktree.
    MarkDoneFromMergedPr { store_id: i64 },
    /// Dead review session — reset to needs_review.
    ResetDeadReview { store_id: i64 },
    /// No automatic fix possible.
    None,
}

/// A single diagnostic finding from `orch service doctor`.
struct Finding {
    severity: Severity,
    task_id: String,
    message: String,
    fix: FixAction,
}

#[derive(Clone, Copy)]
enum Severity {
    Error,
    Warning,
}

impl Severity {
    fn symbol(self) -> &'static str {
        match self {
            Self::Error => "ERR",
            Self::Warning => "WARN",
        }
    }
}

/// Run all diagnostic checks and print findings.
///
/// When called outside a project directory (no `.orch.yml`), runs across all
/// repos found in the store. When called inside a project, scopes to that repo.
pub async fn run(full: bool, fix: bool, dry_run: bool) -> anyhow::Result<()> {
    let store = Arc::new(crate::cli::init_store().await?);
    let gh = GhHttp::new()?;
    let tmux = TmuxManager::new();

    // Resolve repos to check: current project if available, otherwise all repos in store.
    let repos: Vec<String> = if let Ok(repo) = config::get_current_repo() {
        vec![repo]
    } else {
        let all = store.distinct_repos().await?;
        if all.is_empty() {
            println!("No tasks found in store.");
            return Ok(());
        }
        all
    };

    // Spinner: show progress on stderr while checks run (erase with \r on done).
    let spinner_running = Arc::new(AtomicBool::new(true));
    let spinner_flag = std::sync::Arc::clone(&spinner_running);
    let spinner_task = tokio::spawn(async move {
        let frames = ["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
        let mut i = 0usize;
        while spinner_flag.load(Ordering::Relaxed) {
            eprint!(
                "\r{} Running orch service doctor…",
                frames[i % frames.len()]
            );
            let _ = std::io::stderr().flush();
            tokio::time::sleep(std::time::Duration::from_millis(80)).await;
            i += 1;
        }
        eprint!("\r");
        let _ = std::io::stderr().flush();
    });

    let result = run_checks(full, fix, dry_run, &repos, &store, &gh, &tmux).await;

    spinner_running.store(false, Ordering::Relaxed);
    let _ = spinner_task.await;

    result
}

async fn run_checks(
    full: bool,
    fix: bool,
    dry_run: bool,
    repos: &[String],
    store: &Arc<TaskStore>,
    gh: &GhHttp,
    tmux: &TmuxManager,
) -> anyhow::Result<()> {
    let mut all_findings: Vec<Finding> = Vec::new();

    for repo in repos {
        let backend: Arc<dyn ExternalBackend> = Arc::new(GitHubBackend::new(repo.clone())?);
        let mut findings: Vec<Finding> = Vec::new();
        if full {
            // Existing expensive path: load active + recent done tasks and batch GraphQL queries.
            // Only load active tasks + done tasks from the last 7 days — avoids
            // fetching hundreds of historical done tasks on every run.
            let cutoff = chrono::Utc::now() - chrono::Duration::days(7);
            let cutoff_str = cutoff.format("%Y-%m-%dT%H:%M:%SZ").to_string();
            let all_tasks = store.list_for_doctor(repo, &cutoff_str).await?;

            let recent_done_tasks: Vec<_> = all_tasks
                .iter()
                .filter(|t| t.status == TaskStatus::Done)
                .collect();
            let active_tasks: Vec<_> = all_tasks
                .iter()
                .filter(|t| t.status != TaskStatus::Done)
                .collect();
            let in_progress_tasks: Vec<_> = all_tasks
                .iter()
                .filter(|t| t.status == TaskStatus::InProgress)
                .collect();
            let in_review_tasks: Vec<_> = all_tasks
                .iter()
                .filter(|t| t.status == TaskStatus::InReview)
                .collect();

            // Batch-fetch all PR states needed for checks 1 and 8 in a single GraphQL call.
            let pr_numbers_to_fetch: Vec<u64> = {
                let mut nums: Vec<u64> = recent_done_tasks
                    .iter()
                    .filter(|t| !(t.origin == "internal" && t.external_id.is_none()))
                    .filter_map(|t| t.pr_number.and_then(|n| u64::try_from(n).ok()))
                    .chain(
                        active_tasks
                            .iter()
                            .filter_map(|t| t.pr_number.and_then(|n| u64::try_from(n).ok())),
                    )
                    .collect();
                nums.sort_unstable();
                nums.dedup();
                nums
            };
            let pr_states = gh
                .batch_get_pr_states(repo, &pr_numbers_to_fetch)
                .await
                .unwrap_or_default();

            // 1. Done tasks with no merged PR (recent only — skip internal no-PR tasks)
            for task in &recent_done_tasks {
                if task.origin == "internal" && task.external_id.is_none() {
                    continue;
                }
                if task.pr_number.is_none() && task.external_id.is_none() {
                    continue;
                }
                check_done_no_merged_pr(task, gh, &pr_states, &mut findings, repo).await;
            }

            // 2. Done tasks with dirty worktrees (recent only — filesystem check, fast)
            for task in &recent_done_tasks {
                check_dirty_worktree(task, &mut findings).await;
            }

            // 3. Done tasks with unpushed commits (recent only — filesystem check, fast)
            for task in &recent_done_tasks {
                check_unpushed_commits(task, &mut findings).await;
            }

            // 4+5. Issue status and label checks (active external tasks only).
            // Batch-fetch all issue states and labels in a single GraphQL call.
            let external_active: Vec<_> = active_tasks
                .iter()
                .copied()
                .filter(|t| t.origin != "internal")
                .collect();
            let issue_numbers = collect_valid_external_issue_numbers(
                external_active.iter().copied(),
                repo,
                "cli::doctor::run_checks(full)",
            );
            let issue_states = gh
                .batch_get_issue_states(repo, &issue_numbers, "cli::doctor::run_checks(full)")
                .await
                .unwrap_or_default();
            for task in &external_active {
                check_issue_status_mismatch(task, &issue_states, &mut findings);
                check_label_mismatch(task, &issue_states, &mut findings);
            }

            // 6. Stale in_progress tasks (no tmux session)
            for task in &in_progress_tasks {
                check_stale_in_progress(task, repo, tmux, &mut findings).await;
            }

            // 7. Orphaned worktrees (needs all tasks to match worktree paths to owners)
            check_orphaned_worktrees(&all_tasks, &mut findings).await;

            // 8. PR merged but task not done (active tasks only — uses batched pr_states)
            for task in &active_tasks {
                check_pr_merged_not_done(task, &pr_states, &mut findings);
            }

            // 9. Dead review sessions
            for task in &in_review_tasks {
                check_dead_review_session(task, repo, tmux, &mut findings).await;
            }
        } else {
            // Fast path: only consider active (non-done) tasks and open PRs via REST.
            let active_tasks = store.list_active(repo).await?;

            // Fetch open PRs for the repo (paginated REST call)
            let open_prs: Vec<serde_json::Value> =
                gh.list_open_pulls(repo).await.unwrap_or_default();

            // Build lookup maps: pr_number -> pr, head_ref -> pr
            let mut pr_by_number: std::collections::HashMap<u64, serde_json::Value> =
                std::collections::HashMap::new();
            let mut pr_by_head: std::collections::HashMap<String, serde_json::Value> =
                std::collections::HashMap::new();
            for pr in &open_prs {
                if let Some(n) = pr.get("number").and_then(serde_json::Value::as_u64) {
                    pr_by_number.insert(n, pr.clone());
                }
                if let Some(head) = pr.pointer("/head/ref").and_then(|v| v.as_str()) {
                    pr_by_head.insert(head.to_string(), pr.clone());
                }
            }

            // Active tasks: perform lightweight checks
            let external_active: Vec<_> = active_tasks
                .iter()
                .filter(|t| t.origin != "internal")
                .collect();
            for task in &active_tasks {
                // Stale in_progress
                if task.status == TaskStatus::InProgress {
                    check_stale_in_progress(task, repo, tmux, &mut findings).await;
                }

                // Dead review sessions
                if task.status == TaskStatus::InReview {
                    check_dead_review_session(task, repo, tmux, &mut findings).await;
                }

                // PR merged check for tasks that have a PR recorded — make one REST call per active task (few)
                if let Some(pr_num) = task.pr_number.and_then(|n| u64::try_from(n).ok()) {
                    if let Ok(pr) = gh.get_pr(repo, pr_num).await {
                        if pr.merged.unwrap_or(false) {
                            findings.push(Finding {
                                severity: Severity::Error,
                                task_id: task_label(task),
                                message: format!(
                                    "PR #{} is merged but task status is '{}'",
                                    pr_num,
                                    task.status.as_str()
                                ),
                                fix: FixAction::MarkDoneFromMergedPr { store_id: task.id },
                            });
                        }
                    } else {
                        // Ignore transient failures in fast path; the full path will surface them.
                    }
                } else if !task.branch.is_empty() {
                    // If task has a branch, check if there's an open PR for it
                    if let Some(pr) = pr_by_head.get(&task.branch) {
                        // PR exists and is open — link PR (warning) unless already linked
                        if task.pr_number.is_none()
                            && let Some(n) = pr.get("number").and_then(serde_json::Value::as_u64)
                        {
                            findings.push(Finding {
                                severity: Severity::Warning,
                                task_id: task_label(task),
                                message: format!(
                                    "branch '{}' has open PR #{} not linked in store",
                                    task.branch, n
                                ),
                                fix: FixAction::LinkPr {
                                    store_id: task.id,
                                    pr_number: n,
                                },
                            });
                        }
                    }
                }
            }

            // Batch issue state/label checks for external active tasks
            let external_issue_numbers = collect_valid_external_issue_numbers(
                external_active.iter().copied(),
                repo,
                "cli::doctor::run_checks(fast)",
            );
            let issue_states = gh
                .batch_get_issue_states(
                    repo,
                    &external_issue_numbers,
                    "cli::doctor::run_checks(fast)",
                )
                .await
                .unwrap_or_default();
            for task in &external_active {
                check_issue_status_mismatch(task, &issue_states, &mut findings);
                check_label_mismatch(task, &issue_states, &mut findings);
            }

            // Orphaned PRs: open PRs that don't match any active task by number or head ref
            for pr in &open_prs {
                let pr_num = pr.get("number").and_then(serde_json::Value::as_u64);
                let head = pr
                    .pointer("/head/ref")
                    .and_then(|v| v.as_str())
                    .map(std::string::ToString::to_string);
                let mut owned = false;
                if let Some(n) = pr_num {
                    for t in &active_tasks {
                        if let Some(pn) = t.pr_number
                            && u64::try_from(pn) == Ok(n)
                        {
                            owned = true;
                            break;
                        }
                        if !t.branch.is_empty() && Some(t.branch.clone()) == head {
                            owned = true;
                            break;
                        }
                    }
                }
                if !owned {
                    let num_str = pr_num.map_or_else(|| "?".to_string(), |n| n.to_string());
                    findings.push(Finding {
                        severity: Severity::Warning,
                        task_id: format!("pr:{num_str}"),
                        message: format!("open PR with no active task: #{num_str}"),
                        fix: FixAction::None,
                    });
                }
            }

            // A done task still owns its worktree, so include every task here
            let owners = store.list_all(repo).await?;
            check_orphaned_worktrees(&owners, &mut findings).await;
        }

        if repos.len() > 1 && !findings.is_empty() {
            println!("\n=== {repo} ===");
        }

        // Apply per-repo fixes immediately so store_id lookups are in scope.
        if (fix || dry_run) && !findings.is_empty() {
            let errors = findings
                .iter()
                .filter(|f| matches!(f.severity, Severity::Error))
                .count();
            let warnings = findings.len() - errors;
            for f in &findings {
                println!("[{}] #{}: {}", f.severity.symbol(), f.task_id, f.message);
            }
            println!(
                "\nFound {} issue(s): {} error(s), {} warning(s)",
                findings.len(),
                errors,
                warnings,
            );
            apply_fixes(&findings, store, repo, &backend, gh, dry_run).await?;
        }

        all_findings.extend(findings);
    }

    if all_findings.is_empty() {
        println!("No issues found. All task state is consistent.");
        return Ok(());
    }

    // If we didn't already print+fix per-repo above (non-fix mode), print summary now.
    if !fix && !dry_run {
        let errors = all_findings
            .iter()
            .filter(|f| matches!(f.severity, Severity::Error))
            .count();
        let warnings = all_findings.len() - errors;

        for f in &all_findings {
            println!("[{}] #{}: {}", f.severity.symbol(), f.task_id, f.message);
        }

        println!(
            "\nFound {} issue(s): {} error(s), {} warning(s)",
            all_findings.len(),
            errors,
            warnings,
        );

        if errors > 0 {
            println!("\nRun `orch service doctor --fix` to attempt automatic repairs.");
            println!("Run `orch service doctor --dry-run` to preview what --fix would do.");
        }
    }

    Ok(())
}

/// Check 1: Done task with no merged PR.
/// `pr_states` is a pre-fetched cache of pr_number → (merged, state).
async fn check_done_no_merged_pr(
    task: &Task,
    gh: &GhHttp,
    pr_states: &std::collections::HashMap<u64, (bool, String)>,
    findings: &mut Vec<Finding>,
    repo: &str,
) {
    let task_label = task_label(task);
    let store_id = task.id;

    match task.pr_number.and_then(|n| u64::try_from(n).ok()) {
        Some(pr_num) => {
            // Use cached state; fall back to live fetch if missing (e.g. new PR since batch)
            let (merged, state) = if let Some(s) = pr_states.get(&pr_num) {
                s.clone()
            } else {
                match gh.get_pr(repo, pr_num).await {
                    Ok(pr) => (pr.merged.unwrap_or(false), pr.state),
                    Err(e) => {
                        findings.push(Finding {
                            severity: Severity::Warning,
                            task_id: task_label,
                            message: format!("done with PR #{pr_num} but failed to fetch PR: {e}"),
                            fix: FixAction::None,
                        });
                        return;
                    }
                }
            };
            if !merged {
                findings.push(Finding {
                    severity: Severity::Error,
                    task_id: task_label,
                    message: format!(
                        "done but PR #{pr_num} is {state} (not merged) — done is terminal, file a new task to finish the work"
                    ),
                    fix: FixAction::None,
                });
            }
        }
        None => {
            // No PR recorded — check if branch has a PR
            if task.branch.is_empty() {
                findings.push(Finding {
                    severity: Severity::Error,
                    task_id: task_label,
                    message: "done but no branch or PR recorded".to_string(),
                    fix: FixAction::None,
                });
            } else {
                match gh.get_pr_number(repo, &task.branch).await {
                    Ok(Some(pr_num)) => {
                        // PR exists on GitHub but not linked — check merge state
                        let merged = gh
                            .get_pr(repo, pr_num)
                            .await
                            .is_ok_and(|pr| pr.merged == Some(true));
                        if merged {
                            // PR is merged — just link it
                            findings.push(Finding {
                                severity: Severity::Warning,
                                task_id: task_label,
                                message: format!(
                                    "done with no pr_number but branch has merged PR #{pr_num}"
                                ),
                                fix: FixAction::LinkPr {
                                    store_id,
                                    pr_number: pr_num,
                                },
                            });
                        } else {
                            // PR not merged — shouldn't be done
                            findings.push(Finding {
                                severity: Severity::Error,
                                task_id: task_label,
                                message: format!(
                                    "done with no pr_number but branch has unmerged PR #{pr_num} — done is terminal, file a new task to finish the work"
                                ),
                                fix: FixAction::None,
                            });
                        }
                    }
                    Ok(None) => {
                        findings.push(Finding {
                            severity: Severity::Error,
                            task_id: task_label,
                            message: describe_unrecovered_work(task).await,
                            fix: FixAction::None,
                        });
                    }
                    Err(_) => {
                        findings.push(Finding {
                            severity: Severity::Error,
                            task_id: task_label,
                            message: "done but no PR number recorded and branch lookup failed"
                                .to_string(),
                            fix: FixAction::None,
                        });
                    }
                }
            }
        }
    }
}

/// Describe what a done task with no PR left behind in its worktree.
///
/// Report only: the status stays done, so the message tells the operator what
/// work is sitting there and would otherwise be lost (#3780)
async fn describe_unrecovered_work(task: &Task) -> String {
    const HEAD: &str = "done but no PR was ever created";
    if task.worktree.is_empty() || task.worktree_cleaned {
        return format!("{HEAD} and the worktree is gone — any work is lost");
    }
    let wt = Path::new(&task.worktree);
    if !wt.exists() || !wt.join(".git").exists() {
        return format!("{HEAD} and the worktree is gone — any work is lost");
    }

    // Check for dirty files
    let has_dirty = tokio::process::Command::new("git")
        .args(["status", "--porcelain"])
        .current_dir(wt)
        .output()
        .await
        .is_ok_and(|o| !o.stdout.is_empty());

    if has_dirty {
        return format!("{HEAD}; uncommitted changes left in {}", task.worktree);
    }

    // Check for unpushed commits
    let has_unpushed = tokio::process::Command::new("git")
        .args(["log", &format!("origin/{}..HEAD", task.branch), "--oneline"])
        .current_dir(wt)
        .output()
        .await
        .is_ok_and(|o| !o.stdout.is_empty());

    if has_unpushed {
        return format!("{HEAD}; unpushed commits left in {}", task.worktree);
    }

    // Branch pushed, no PR
    let branch_on_remote = crate::engine::runner::git_ops::git()
        .await
        .args(["ls-remote", "--heads", "origin", &task.branch])
        .current_dir(wt)
        .output()
        .await
        .is_ok_and(|o| !o.stdout.is_empty());

    if branch_on_remote {
        return format!("{HEAD}; branch '{}' is pushed with no PR", task.branch);
    }

    HEAD.to_string()
}

/// Check 2: Done task with dirty worktree (uncommitted changes).
async fn check_dirty_worktree(task: &Task, findings: &mut Vec<Finding>) {
    if task.worktree.is_empty() || task.worktree_cleaned {
        return;
    }
    let wt = Path::new(&task.worktree);
    if !wt.exists() || !wt.join(".git").exists() {
        return;
    }
    let output = tokio::process::Command::new("git")
        .args(["status", "--porcelain"])
        .current_dir(wt)
        .output()
        .await;
    if let Ok(out) = output
        && !out.stdout.is_empty()
    {
        findings.push(Finding {
                severity: Severity::Error,
                task_id: task_label(task),
                message: format!(
                    "done but worktree has uncommitted changes: {} — done is terminal, file a new task to land them",
                    task.worktree
                ),
                fix: FixAction::None,
            });
    }
}

/// Check 3: Done task with unpushed commits.
async fn check_unpushed_commits(task: &Task, findings: &mut Vec<Finding>) {
    if task.worktree.is_empty() || task.worktree_cleaned || task.branch.is_empty() {
        return;
    }
    let wt = Path::new(&task.worktree);
    if !wt.exists() || !wt.join(".git").exists() {
        return;
    }
    let output = tokio::process::Command::new("git")
        .args(["log", &format!("origin/{}..HEAD", task.branch), "--oneline"])
        .current_dir(wt)
        .output()
        .await;
    if let Ok(out) = output
        && !out.stdout.is_empty()
    {
        #[expect(
            clippy::naive_bytecount,
            reason = "a short git log does not need the bytecount crate"
        )]
        let count = out.stdout.iter().filter(|&&b| b == b'\n').count();
        findings.push(Finding {
                severity: Severity::Error,
                task_id: task_label(task),
                message: format!(
                    "done but {} unpushed commit(s) in worktree: {} — done is terminal, file a new task to land them",
                    count, task.worktree
                ),
                fix: FixAction::None,
            });
    }
}

/// Check 4: Closed GitHub issue with non-done SQLite status (and vice versa).
fn check_issue_status_mismatch(
    task: &Task,
    issue_states: &std::collections::HashMap<String, (String, Vec<String>)>,
    findings: &mut Vec<Finding>,
) {
    let ext_id = match &task.external_id {
        Some(id) => id.clone(),
        None => return,
    };

    let Some((state, _labels)) = issue_states.get(&ext_id) else {
        return;
    };

    let issue_closed = state == "closed";
    let task_done = task.status == TaskStatus::Done;
    let task_blocked = task.status == TaskStatus::Blocked;

    if issue_closed && !task_done && !task_blocked {
        findings.push(Finding {
            severity: Severity::Error,
            task_id: task_label(task),
            message: format!(
                "GitHub issue is closed but SQLite status is '{}'",
                task.status.as_str()
            ),
            fix: FixAction::ReopenIssue { store_id: task.id },
        });
    } else if !issue_closed && task_done {
        findings.push(Finding {
            severity: Severity::Warning,
            task_id: task_label(task),
            message: "SQLite status is 'done' but GitHub issue is still open".to_string(),
            fix: FixAction::CloseIssue { store_id: task.id },
        });
    }
}

/// Check 5: Label/status mismatch.
fn check_label_mismatch(
    task: &Task,
    issue_states: &std::collections::HashMap<String, (String, Vec<String>)>,
    findings: &mut Vec<Finding>,
) {
    let ext_id = match &task.external_id {
        Some(id) => id.clone(),
        None => return,
    };

    let Some((_state, labels)) = issue_states.get(&ext_id) else {
        return;
    };

    let expected_label = format!("status:{}", task.status.as_str());
    let has_expected = labels.iter().any(|l| l == &expected_label);
    let status_labels: Vec<_> = labels.iter().filter(|l| l.starts_with("status:")).collect();

    if !has_expected {
        let actual = if status_labels.is_empty() {
            "none".to_string()
        } else {
            status_labels
                .iter()
                .map(|s| s.as_str())
                .collect::<Vec<_>>()
                .join(", ")
        };
        findings.push(Finding {
            severity: Severity::Warning,
            task_id: task_label(task),
            message: format!(
                "label mismatch: SQLite='{}' but GitHub labels=[{}]",
                task.status.as_str(),
                actual
            ),
            fix: FixAction::SyncLabels { store_id: task.id },
        });
    }
}

/// Check 6: Stale in_progress task (no tmux session).
async fn check_stale_in_progress(
    task: &Task,
    repo: &str,
    tmux: &TmuxManager,
    findings: &mut Vec<Finding>,
) {
    let task_id_str = match &task.external_id {
        Some(id) => id.clone(),
        None => format!("internal:{}", task.id),
    };
    let session = tmux.session_name(repo, &task_id_str);
    if !tmux.session_exists(&session).await {
        findings.push(Finding {
            severity: Severity::Error,
            task_id: task_label(task),
            message: format!("status is 'in_progress' but no tmux session '{session}' found"),
            fix: FixAction::ResetToRouted { store_id: task.id },
        });
    }
}

/// Check 7: Orphaned worktrees.
async fn check_orphaned_worktrees(all_tasks: &[Task], findings: &mut Vec<Finding>) {
    let Ok(worktrees_dir) = crate::home::worktrees_dir() else {
        return;
    };
    check_orphaned_worktrees_in(&worktrees_dir, all_tasks, findings).await;
}

async fn check_orphaned_worktrees_in(
    worktrees_dir: &Path,
    all_tasks: &[Task],
    findings: &mut Vec<Finding>,
) {
    let Ok(project_dirs) = std::fs::read_dir(worktrees_dir) else {
        return;
    };

    // Build a HashMap for O(1) worktree-path → task lookups instead of O(T) linear scan.
    let task_by_worktree: std::collections::HashMap<&str, &Task> = all_tasks
        .iter()
        .filter(|t| !t.worktree.is_empty())
        .map(|t| (t.worktree.as_str(), t))
        .collect();

    for project_entry in project_dirs {
        let project_entry = match project_entry {
            Ok(e) => e,
            Err(e) => {
                tracing::warn!(err = %e, "error reading worktrees directory entry");
                continue;
            }
        };
        if !project_entry.file_type().is_ok_and(|t| t.is_dir()) {
            continue;
        }
        let Ok(branch_dirs) = std::fs::read_dir(project_entry.path()) else {
            continue;
        };
        for branch_entry in branch_dirs {
            let branch_entry = match branch_entry {
                Ok(e) => e,
                Err(e) => {
                    tracing::warn!(err = %e, "error reading project directory entry");
                    continue;
                }
            };
            if !branch_entry.file_type().is_ok_and(|t| t.is_dir()) {
                continue;
            }
            let wt_path = branch_entry.path().to_string_lossy().to_string();

            let owning_task = task_by_worktree.get(wt_path.as_str()).copied();

            match owning_task {
                Some(task) => {
                    if task.status == TaskStatus::Done && !task.worktree_cleaned {
                        // Check if worktree has uncommitted/unpushed work
                        let has_work = worktree_has_work(Path::new(&wt_path), &task.branch).await;
                        if has_work {
                            // Don't auto-clean — there's work to save
                            findings.push(Finding {
                                severity: Severity::Warning,
                                task_id: task_label(task),
                                message: format!("done but worktree has unsaved work: {wt_path}"),
                                fix: FixAction::None,
                            });
                        } else {
                            findings.push(Finding {
                                severity: Severity::Warning,
                                task_id: task_label(task),
                                message: format!("done but worktree not cleaned up: {wt_path}"),
                                fix: FixAction::CleanWorktree { store_id: task.id },
                            });
                        }
                    }
                }
                None => {
                    findings.push(Finding {
                        severity: Severity::Warning,
                        task_id: "?".to_string(),
                        message: format!("orphaned worktree (no task owns it): {wt_path}"),
                        fix: FixAction::RemoveOrphanedWorktree {
                            path: wt_path.clone(),
                        },
                    });
                }
            }
        }
    }
}

/// Check 8: PR merged but task not done (uses pre-fetched pr_states cache).
fn check_pr_merged_not_done(
    task: &Task,
    pr_states: &std::collections::HashMap<u64, (bool, String)>,
    findings: &mut Vec<Finding>,
) {
    let Some(pr_num) = task.pr_number.and_then(|n| u64::try_from(n).ok()) else {
        return;
    };

    if let Some((merged, _)) = pr_states.get(&pr_num)
        && *merged
    {
        findings.push(Finding {
            severity: Severity::Error,
            task_id: task_label(task),
            message: format!(
                "PR #{} is merged but task status is '{}'",
                pr_num,
                task.status.as_str()
            ),
            fix: FixAction::MarkDoneFromMergedPr { store_id: task.id },
        });
    }
}

/// Check 9: Dead review sessions. Callers pass only in_review tasks.
async fn check_dead_review_session(
    task: &Task,
    repo: &str,
    tmux: &TmuxManager,
    findings: &mut Vec<Finding>,
) {
    let task_id_str = match &task.external_id {
        Some(id) => id.clone(),
        None => format!("internal:{}", task.id),
    };
    let review_task_id = format!("{task_id_str}-review");
    let session = tmux.session_name(repo, &review_task_id);
    if !tmux.session_exists(&session).await {
        findings.push(Finding {
            severity: Severity::Error,
            task_id: task_label(task),
            message: format!("status is 'in_review' but no review session '{session}' found"),
            fix: FixAction::ResetDeadReview { store_id: task.id },
        });
    }
}

/// Check if a worktree has uncommitted changes or unpushed commits.
async fn worktree_has_work(wt: &Path, branch: &str) -> bool {
    if !wt.join(".git").exists() {
        return false;
    }
    let has_dirty = tokio::process::Command::new("git")
        .args(["status", "--porcelain"])
        .current_dir(wt)
        .output()
        .await
        .is_ok_and(|o| !o.stdout.is_empty());
    if has_dirty {
        return true;
    }
    if !branch.is_empty() {
        let has_unpushed = tokio::process::Command::new("git")
            .args(["log", &format!("origin/{branch}..HEAD"), "--oneline"])
            .current_dir(wt)
            .output()
            .await
            .is_ok_and(|o| !o.stdout.is_empty());
        if has_unpushed {
            return true;
        }
    }
    false
}

/// Attempt automatic fixes for known issues.
async fn apply_fixes(
    findings: &[Finding],
    store: &Arc<TaskStore>,
    repo: &str,
    backend: &Arc<dyn ExternalBackend>,
    gh: &GhHttp,
    dry_run: bool,
) -> anyhow::Result<()> {
    let prefix = if dry_run { "[dry-run] " } else { "" };
    let mut fixed = 0;
    let mut skipped = 0;

    for f in findings {
        match &f.fix {
            FixAction::None => {
                skipped += 1;
            }
            FixAction::LinkPr {
                store_id,
                pr_number,
            } => {
                if dry_run {
                    println!(
                        "  {}would link PR #{} to task #{}",
                        prefix, pr_number, f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                let _ = store
                    .set_fields(*store_id, &[("pr_number", serde_json::json!(*pr_number))])
                    .await;
                println!("  fixed #{}: linked PR #{}", f.task_id, pr_number);
                fixed += 1;
            }
            FixAction::ReopenIssue { store_id } => {
                let task = store.get(*store_id).await?;

                if dry_run {
                    println!(
                        "  {}would reopen GitHub issue + sync labels for #{}",
                        prefix, f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                if let Some(ref ext_id) = task.external_id {
                    if let Err(e) = gh.reopen_issue(repo, ext_id).await {
                        eprintln!("  fix failed for #{}: reopen failed: {}", f.task_id, e);
                        skipped += 1;
                        continue;
                    }
                    let status = task_status_to_backend_status(task.status);
                    let _ = backend
                        .update_status(&ExternalId(ext_id.clone()), status)
                        .await;
                    println!("  fixed #{}: reopened issue + synced labels", f.task_id);
                    fixed += 1;
                } else {
                    skipped += 1;
                }
            }
            FixAction::CloseIssue { store_id } => {
                let task = store.get(*store_id).await?;

                if dry_run {
                    println!("  {}would close GitHub issue #{}", prefix, f.task_id);
                    fixed += 1;
                    continue;
                }

                if let Some(ref ext_id) = task.external_id {
                    let status = crate::backends::Status::Done;
                    if let Err(e) = backend
                        .update_status(&ExternalId(ext_id.clone()), status)
                        .await
                    {
                        eprintln!("  fix failed for #{}: {}", f.task_id, e);
                        skipped += 1;
                    } else {
                        println!("  fixed #{}: closed GitHub issue", f.task_id);
                        fixed += 1;
                    }
                } else {
                    skipped += 1;
                }
            }
            FixAction::SyncLabels { store_id } => {
                let task = store.get(*store_id).await?;

                if dry_run {
                    println!(
                        "  {}would sync labels to status:{} for #{}",
                        prefix,
                        task.status.as_str(),
                        f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                if let Some(ref ext_id) = task.external_id {
                    let status = task_status_to_backend_status(task.status);
                    if let Err(e) = backend
                        .update_status(&ExternalId(ext_id.clone()), status)
                        .await
                    {
                        eprintln!("  fix failed for #{}: {}", f.task_id, e);
                        skipped += 1;
                    } else {
                        println!("  fixed #{}: synced labels", f.task_id);
                        fixed += 1;
                    }
                } else {
                    skipped += 1;
                }
            }
            FixAction::ResetToRouted { store_id } => {
                if dry_run {
                    println!(
                        "  {}would reset #{} to 'routed' (re-dispatch on next tick)",
                        prefix, f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                if let Err(e) = store.update_status(*store_id, TaskStatus::Routed).await {
                    eprintln!("  fix failed for #{}: {}", f.task_id, e);
                    skipped += 1;
                    continue;
                }

                // Sync labels if external
                let task = store.get(*store_id).await?;
                if let Some(ref ext_id) = task.external_id {
                    let _ = backend
                        .update_status(&ExternalId(ext_id.clone()), crate::backends::Status::Routed)
                        .await;
                }
                println!("  fixed #{}: reset to routed", f.task_id);
                fixed += 1;
            }
            FixAction::CleanWorktree { store_id } => {
                let task = store.get(*store_id).await?;

                if dry_run {
                    println!(
                        "  {}would clean worktree + mark cleaned for #{}",
                        prefix, f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                let wt = Path::new(&task.worktree);
                if wt.exists() {
                    match resolve_repo_root(repo).await {
                        Ok(root) => {
                            let branch = if task.branch.is_empty() {
                                None
                            } else {
                                Some(task.branch.as_str())
                            };
                            let removed = remove_worktree_and_branch(
                                &f.task_id,
                                wt,
                                branch,
                                Path::new(&root),
                                task.pr_number.is_some(), // keep remote branch if PR exists
                            )
                            .await;
                            if removed {
                                let _ = store.mark_cleaned(*store_id).await;
                                println!("  fixed #{}: cleaned worktree", f.task_id);
                                fixed += 1;
                            } else {
                                eprintln!(
                                    "  fix failed for #{}: worktree removal failed",
                                    f.task_id
                                );
                                skipped += 1;
                            }
                        }
                        Err(e) => {
                            eprintln!(
                                "  fix failed for #{}: cannot resolve repo root: {}",
                                f.task_id, e
                            );
                            skipped += 1;
                        }
                    }
                } else {
                    // Directory already gone — just mark cleaned
                    let _ = store.mark_cleaned(*store_id).await;
                    println!(
                        "  fixed #{}: marked worktree cleaned (already gone)",
                        f.task_id
                    );
                    fixed += 1;
                }
            }
            FixAction::RemoveOrphanedWorktree { path } => {
                if dry_run {
                    println!("  {prefix}would remove orphaned worktree: {path}");
                    fixed += 1;
                    continue;
                }

                let removed = cleanup_orphaned_worktree(&f.task_id, Path::new(path)).await;
                if removed {
                    println!("  fixed: removed orphaned worktree {path}");
                    fixed += 1;
                } else {
                    eprintln!("  fix failed: could not remove orphaned worktree {path}");
                    skipped += 1;
                }
            }
            FixAction::MarkDoneFromMergedPr { store_id } => {
                let task = store.get(*store_id).await?;

                if dry_run {
                    println!(
                        "  {}would mark #{} done + close issue + clean worktree",
                        prefix, f.task_id
                    );
                    fixed += 1;
                    continue;
                }

                // Set status to done
                if let Err(e) = store.update_status(*store_id, TaskStatus::Done).await {
                    eprintln!("  fix failed for #{}: {}", f.task_id, e);
                    skipped += 1;
                    continue;
                }

                // Close GitHub issue + sync labels
                if let Some(ref ext_id) = task.external_id {
                    let _ = backend
                        .update_status(&ExternalId(ext_id.clone()), crate::backends::Status::Done)
                        .await;
                }

                // Clean worktree if present
                if !task.worktree.is_empty() && !task.worktree_cleaned {
                    let wt = Path::new(&task.worktree);
                    if wt.exists() {
                        if let Ok(root) = resolve_repo_root(repo).await {
                            let branch = if task.branch.is_empty() {
                                None
                            } else {
                                Some(task.branch.as_str())
                            };
                            let removed = remove_worktree_and_branch(
                                &f.task_id,
                                wt,
                                branch,
                                Path::new(&root),
                                true, // keep remote — PR is merged
                            )
                            .await;
                            if removed {
                                let _ = store.mark_cleaned(*store_id).await;
                            }
                        }
                    } else {
                        let _ = store.mark_cleaned(*store_id).await;
                    }
                }

                println!("  fixed #{}: marked done + closed issue", f.task_id);
                fixed += 1;
            }
            FixAction::ResetDeadReview { store_id } => {
                if dry_run {
                    println!("  {}would set #{} needs_review", prefix, f.task_id);
                    fixed += 1;
                    continue;
                }

                if let Err(e) = store
                    .update_status(*store_id, TaskStatus::NeedsReview)
                    .await
                {
                    eprintln!("  fix failed for #{}: {}", f.task_id, e);
                    skipped += 1;
                    continue;
                }

                // Sync labels
                let task = store.get(*store_id).await?;
                if let Some(ref ext_id) = task.external_id {
                    let _ = backend
                        .update_status(
                            &ExternalId(ext_id.clone()),
                            crate::backends::Status::NeedsReview,
                        )
                        .await;
                }
                println!(
                    "  fixed #{}: reset dead review session + set needs_review",
                    f.task_id
                );
                fixed += 1;
            }
        }
    }

    let action = if dry_run { "would fix" } else { "fixed" };
    println!("\n{action} {fixed}, skipped {skipped}.");

    if !dry_run && skipped > 0 {
        println!("Reported issues with no automatic fix need a new issue or task.");
    }

    Ok(())
}

fn task_label(task: &Task) -> String {
    match &task.external_id {
        Some(id) => id.clone(),
        None => format!("internal:{}", task.id),
    }
}

fn task_status_to_backend_status(status: TaskStatus) -> crate::backends::Status {
    match status {
        TaskStatus::New => crate::backends::Status::New,
        TaskStatus::Routed => crate::backends::Status::Routed,
        TaskStatus::InProgress => crate::backends::Status::InProgress,
        TaskStatus::Done => crate::backends::Status::Done,
        TaskStatus::Blocked => crate::backends::Status::Blocked,
        TaskStatus::InReview => crate::backends::Status::InReview,
        TaskStatus::Approved => crate::backends::Status::Approved,
        TaskStatus::NeedsReview => crate::backends::Status::NeedsReview,
        TaskStatus::Waiting => crate::backends::Status::Waiting,
    }
}

fn collect_valid_external_issue_numbers<'a>(
    tasks: impl IntoIterator<Item = &'a Task>,
    repo: &str,
    caller_context: &str,
) -> Vec<u64> {
    let mut issue_numbers = Vec::new();

    for task in tasks {
        let Some(external_id) = task.external_id.as_deref() else {
            continue;
        };

        match external_id.parse::<u64>() {
            Ok(0) => {
                tracing::warn!(
                    repo,
                    caller_context,
                    store_id = task.id,
                    external_id,
                    "dropping invalid external_id before batch issue-state query"
                );
            }
            Ok(issue_number) => issue_numbers.push(issue_number),
            Err(error) => {
                tracing::warn!(
                    repo,
                    caller_context,
                    store_id = task.id,
                    external_id,
                    error = %error,
                    "skipping non-numeric external_id in batch issue-state query"
                );
            }
        }
    }

    issue_numbers.sort_unstable();
    issue_numbers.dedup();
    issue_numbers
}

#[cfg(test)]
mod tests {
    use super::collect_valid_external_issue_numbers;
    use crate::store::{Task, TaskStatus};

    fn task(id: i64, external_id: Option<&str>, origin: &str) -> Task {
        Task {
            id,
            external_id: external_id.map(ToOwned::to_owned),
            repo: "owner/repo".to_string(),
            origin: origin.to_string(),
            title: String::new(),
            body: String::new(),
            status: TaskStatus::New,
            source: String::new(),
            source_id: String::new(),
            author: String::new(),
            url: String::new(),
            labels: Vec::new(),
            agent: None,
            model: None,
            complexity: String::new(),
            estimate: 0,
            route_reason: String::new(),
            agent_profile: String::new(),
            selected_skills: String::new(),
            route_attempts: 0,
            attempts: 0,
            branch: String::new(),
            worktree: String::new(),
            worktree_cleaned: false,
            owner_node: None,
            summary: String::new(),
            last_error: String::new(),
            parent_id: None,
            block_reason: None,
            pr_number: None,
            pr_review_context: String::new(),
            last_review_ts: String::new(),
            review_ts_map: String::new(),
            last_comment_review_ts: String::new(),
            merge_conflict_retries: 0,
            ci_merge_failures: 0,
            pr_create_failures: 0,
            push_failures: 0,
            network_retries: 0,
            review_agent_failures: 0,
            review_resets: 0,
            review_cycles: 0,
            review_invocations: 0,
            needs_review_refires: 0,
            input_tokens: 0,
            output_tokens: 0,
            input_cost_usd: 0.0,
            output_cost_usd: 0.0,
            total_cost_usd: 0.0,
            model_reroute_chain: String::new(),
            limit_reroute_chain: String::new(),
            memory: Vec::new(),
            delegations: Vec::new(),
            auto_unblock_count: 0,
            auto_unblock_last_at: String::new(),
            auto_unblock_last_reason: String::new(),
            ci_recovery_count: 0,
            no_code_reroutes: 0,
            no_code_last_agent: String::new(),
            created_at: String::new(),
            updated_at: String::new(),
        }
    }

    #[tokio::test]
    async fn done_task_worktree_is_not_reported_as_orphaned() {
        let base = tempfile::tempdir().unwrap();
        let wt = base.path().join("proj").join("branch-1");
        std::fs::create_dir_all(&wt).unwrap();

        let mut done = task(1, Some("1"), "github");
        done.status = TaskStatus::Done;
        done.worktree = wt.to_string_lossy().to_string();

        let mut findings = Vec::new();
        super::check_orphaned_worktrees_in(base.path(), &[done], &mut findings).await;
        assert_eq!(findings.len(), 1);
        assert!(
            findings[0]
                .message
                .contains("done but worktree not cleaned up")
        );
        assert!(!findings[0].message.contains("orphaned"));

        let mut findings = Vec::new();
        super::check_orphaned_worktrees_in(base.path(), &[], &mut findings).await;
        assert!(findings[0].message.contains("orphaned worktree"));
    }

    #[test]
    fn collect_valid_external_issue_numbers_filters_zero_and_non_numeric_ids() {
        let tasks = [
            task(1, Some("42"), "github"),
            task(2, Some("0"), "github"),
            task(3, Some("not-a-number"), "github"),
            task(4, Some("42"), "github"),
        ];

        let issue_numbers =
            collect_valid_external_issue_numbers(tasks.iter(), "owner/repo", "test");

        assert_eq!(issue_numbers, vec![42]);
    }
}

#[cfg(test)]
mod done_is_terminal_tests {
    use super::*;
    use crate::backends::test_helpers::NoopBackend;
    use crate::store::{NewTask, TaskStore};

    fn git(dir: &Path, args: &[&str]) {
        let ok = std::process::Command::new("git")
            .args(args)
            .current_dir(dir)
            .env("GIT_AUTHOR_NAME", "t")
            .env("GIT_AUTHOR_EMAIL", "t@example.com")
            .env("GIT_COMMITTER_NAME", "t")
            .env("GIT_COMMITTER_EMAIL", "t@example.com")
            .output()
            .expect("git runs")
            .status
            .success();
        assert!(ok, "git {args:?} failed");
    }

    /// `doctor --fix` must leave a done task done, even when its worktree still
    /// holds uncommitted work. Follow-up work gets a new task (#3780).
    #[tokio::test]
    async fn fix_leaves_done_task_status_alone() {
        let dir = tempfile::tempdir().unwrap();
        let wt = dir.path();
        git(wt, &["init", "-b", "main"]);
        std::fs::write(wt.join("a.txt"), "a").unwrap();
        git(wt, &["add", "-A"]);
        git(wt, &["commit", "-m", "init"]);
        // Uncommitted change — the state that used to trigger commit + push + needs_review.
        std::fs::write(wt.join("b.txt"), "b").unwrap();

        let store = Arc::new(TaskStore::open_memory().await.unwrap());
        let store_id = store
            .create(&NewTask {
                external_id: Some("58".to_string()),
                repo: "owner/repo".to_string(),
                origin: "github".to_string(),
                title: "Task".to_string(),
                body: String::new(),
                source: "cron".to_string(),
                source_id: "code-development".to_string(),
                author: "bot".to_string(),
                url: String::new(),
                labels: vec![],
                parent_id: None,
            })
            .await
            .unwrap();
        store
            .set_fields(
                store_id,
                &[
                    ("worktree", serde_json::json!(wt.display().to_string())),
                    ("branch", serde_json::json!("main")),
                ],
            )
            .await
            .unwrap();
        store
            .update_status(store_id, TaskStatus::Done)
            .await
            .unwrap();
        let task = store.get(store_id).await.unwrap();

        let mut findings = Vec::new();
        check_dirty_worktree(&task, &mut findings).await;
        check_unpushed_commits(&task, &mut findings).await;
        assert!(
            !findings.is_empty(),
            "a done task with uncommitted work must still be reported"
        );
        for f in &findings {
            assert!(
                matches!(f.fix, FixAction::None),
                "done-task finding must carry no automatic fix: {}",
                f.message
            );
        }

        let backend: Arc<dyn ExternalBackend> = Arc::new(NoopBackend);
        let gh = GhHttp::new().unwrap();
        apply_fixes(&findings, &store, "owner/repo", &backend, &gh, false)
            .await
            .unwrap();

        assert_eq!(
            store.get(store_id).await.unwrap().status,
            TaskStatus::Done,
            "doctor --fix must not move a done task out of done"
        );
    }
}