AGENTS.md

@@ -197,5 +197,14 @@ wrapped per stage (login / read denied / write denied) via `ErrVaultDenied`.
   the worktree goes and the branch stays. `origin/<branch>` is only evidence when
   this run's pruning fetch succeeded; a failed fetch leaves stale tracking refs,
   so those verdicts fall back to keeping the branch.
+- `agentws prune` discovers worktrees from the worktree root *and* from
+  `git worktree list` on each source checkout, merging the two so git's own
+  `locked`/`prunable` flags reach entries the directory scan already found.
+  Removing a worktree is only safe because the local branch keeps its commits, so
+  the cases with no branch to fall back on are kept: a detached HEAD carrying
+  commits on no remote, a locked checkout, or one with a sequencer operation
+  half-finished (`rebase-merge`, `MERGE_HEAD`, `CHERRY_PICK_HEAD`, …). A directory
+  whose backing repo is gone is deleted outright, but only ever inside the
+  worktree root.
 - CI "combined status" comes from `/commits/{sha}/status`; an empty head SHA
   yields an empty state without an API call.

README.md

@@ -104,8 +104,10 @@ agentws list
 agentws rm benvin/my-change
 agentws rm ~/.cache/agentws/argocd-apps__benvin-my-change --delete-branch
 
-# Classify every managed worktree; dry run unless --yes is given
+# Classify every worktree found; dry run unless --yes is given
 agentws prune
+agentws prune --json
+agentws prune --no-fetch
 agentws prune --yes
 agentws prune --yes --keep-branches
 
@@ -118,16 +120,26 @@ agentws token
 
 ### prune
 
-`agentws prune` decides, per worktree, whether its work is safely upstream:
+`agentws prune` finds worktrees two ways and merges the results: the managed
+directories under the worktree root, and `git worktree list` on every source
+checkout — so hand-made worktrees, stale registrations whose directory is gone,
+and leftover directories whose source repo was deleted all show up too.
+
+It then decides, per worktree, whether its work is safely upstream:
 
 | Signal (first match wins) | Verdict |
 |---|---|
-| uncommitted or untracked changes | keep |
+| working tree gone (registration only) | prune the registration |
+| backing repo gone | delete the leftover directory |
+| locked by `git worktree lock` | keep |
+| rebase, merge, cherry-pick, revert or bisect in progress | keep |
+| uncommitted, staged or untracked changes | keep |
 | branch has an open PR | keep |
 | tip contained in `origin/<default>` | remove worktree + local branch |
 | every commit patch-equivalent to one in `origin/<default>`'s history | remove worktree + local branch |
 | PR merged **and** HEAD contained in the PR's head commit (or in a verified `origin/<branch>`) | remove worktree + local branch |
 | PR closed **and** HEAD contained in a verified `origin/<branch>` | remove worktree + local branch |
+| detached HEAD carrying commits on no remote | keep |
 | anything else | remove worktree, keep the branch |
 
 A branch is deleted only where git proves its commits survive elsewhere. PR
@@ -155,7 +167,32 @@ hits the pagination cap is reported rather than read as "no PR". Matching a
 branch to its PR uses `head.label`, since Gitea rewrites `head.ref` to
 `refs/pull/<n>/head` once the branch is deleted on merge.
 
-`--keep-branches` removes worktrees only, and its verdicts print as `remove`.
+The last row is safe only because the local branch keeps the commits, so the
+reason names the branch it is relying on. A detached HEAD has no such branch, so
+unique commits there are kept instead.
+
+Output is a table (`REPO BRANCH PATH VERDICT REASON`) with every verdict's reason
+spelled out, or `--json` for scripting. Neither form needs a terminal.
+
+| Flag | Effect |
+|---|---|
+| `--yes` | apply the plan; without it nothing is touched |
+| `--keep-branches` | remove worktrees only; verdicts print as `remove` |
+| `--no-fetch` | judge against the refs already on disk, for offline use |
+| `--json` | emit the report as JSON on stdout, notes on stderr |
+| `--include-unmanaged` | also remove worktrees outside the worktree root |
+| `--include-keep` | dangerous: also remove worktrees classified `keep`, destroying uncommitted and in-progress work |
+
+Without `--include-unmanaged` a hand-made worktree is reported and then skipped,
+naming the flag that would remove it. `--include-keep` is the only way past a
+`keep`. It leaves the branch, so committed work outlives the worktree, but
+`git worktree remove --force` discards a dirty working tree and a paused
+rebase's sequencer state without a word, and no branch was carrying those.
+
+A directory under the worktree root is deleted outright only when its git dir
+and the repo's shared `.git` are both proven absent by `stat`. When git merely
+fails to answer for a checkout, the verdict is `keep` with the error as its
+reason: an unread state is never a dead one.
 
 ### Auth / credential-helper design
 

cmd/agentws/main.go

@@ -13,7 +13,8 @@
 //	agentws new <repo> [--branch benvin/<name>] [--from <base-branch>]
 //	agentws list
 //	agentws rm <path-or-branch> [--delete-branch]
-//	agentws prune [--yes] [--keep-branches]
+//	agentws prune [--yes] [--keep-branches] [--no-fetch] [--json]
+//	              [--include-unmanaged] [--include-keep]
 //	agentws clean
 //	agentws token
 //	agentws credential get   # git credential-helper protocol on stdin
@@ -25,6 +26,7 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"sort"
 	"strings"
 
 	"git.unkin.net/unkin/agent-tools/internal/agent"
@@ -228,7 +230,14 @@ func newListCmd() *cobra.Command {
 				return nil
 			}
 			for _, w := range managed {
-				_, _ = fmt.Fprintf(out, "%s\t%s\t%s\n", w.repo, w.branch, w.path)
+				branch := w.branch
+				switch {
+				case w.orphan:
+					branch = "(orphan)"
+				case w.inspectErr != nil:
+					branch = "(unreadable)"
+				}
+				_, _ = fmt.Fprintf(out, "%s\t%s\t%s\n", w.repo, branch, w.path)
 			}
 			return nil
 		},
@@ -241,10 +250,31 @@ type managedWt struct {
 	branch string
 	path   string
 	srcDir string
+	// managed is false for worktrees found via `git worktree list` that live
+	// outside the worktree root, i.e. somebody made them by hand.
+	managed bool
+	// detached is true when the worktree has no branch to fall back on, so its
+	// commits die with the checkout.
+	detached bool
+	// locked records git's own "do not remove me" marker.
+	locked bool
+	// missing is a registration whose working tree is gone: nothing to inspect,
+	// nothing to lose.
+	missing bool
+	// orphan is a directory under the worktree root whose backing git dir is
+	// proven gone, so no git state can be read from it ever again.
+	orphan bool
+	// inspectErr is set when git refused to answer for a checkout and the reason
+	// was not a proven-absent backing repo. The state is unknown, never removable.
+	inspectErr error
 }
 
 // managedWorktrees scans the worktree root and resolves each entry's repo and
 // branch from git so branch names are accurate (not the sanitized dir name).
+// Directories whose backing repo is proven gone are returned as orphans rather
+// than dropped, so callers can see (and clean up) the leftovers; a directory git
+// merely failed to answer for is returned with its error instead, because an
+// unread state must never be mistaken for a dead one.
 func managedWorktrees() ([]managedWt, error) {
 	wr, err := worktreeRoot()
 	if err != nil {
@@ -263,24 +293,238 @@ func managedWorktrees() ([]managedWt, error) {
 			continue
 		}
 		path := filepath.Join(wr, e.Name())
-		branch, err := agent.GitCurrentBranch(path)
-		if err != nil {
-			continue // not a git worktree; skip
+		if _, err := os.Stat(filepath.Join(path, ".git")); err != nil {
+			continue // not a worktree checkout at all
 		}
-		srcDir, err := agent.SourceRepoDir(path)
-		if err != nil {
+		branch, branchErr := agent.GitCurrentBranch(path)
+		srcDir, srcErr := agent.SourceRepoDir(path)
+		if branchErr != nil || srcErr != nil {
+			entry := managedWt{repo: repoFromDirName(e.Name()), path: path, managed: true}
+			if gone, err := backingRepoGone(path); err == nil && gone {
+				entry.orphan = true
+			} else if branchErr != nil {
+				entry.inspectErr = branchErr
+			} else {
+				entry.inspectErr = srcErr
+			}
+			out = append(out, entry)
 			continue
 		}
 		out = append(out, managedWt{
-			repo:   filepath.Base(srcDir),
-			branch: branch,
-			path:   path,
-			srcDir: srcDir,
+			repo:     filepath.Base(srcDir),
+			branch:   branch,
+			path:     path,
+			srcDir:   srcDir,
+			managed:  true,
+			detached: branch == "HEAD",
 		})
 	}
 	return out, nil
 }
 
+// backingRepoGone proves, by stat alone, that a worktree directory's backing
+// repo no longer exists: its .git file names a git dir that is absent, and the
+// repo's shared .git the git dir lived in is absent too. Only that pair licenses
+// deleting the directory. Every other outcome — an unreadable .git file, a git
+// dir still on disk, a stat that failed for any reason other than "not there",
+// or a mere lost registration in a repo that is still present — reports false,
+// so a transient or unexplained failure can never be read as "safe to delete".
+func backingRepoGone(path string) (bool, error) {
+	dot := filepath.Join(path, ".git")
+	info, err := os.Lstat(dot)
+	if err != nil {
+		return false, err
+	}
+	if info.IsDir() {
+		return false, nil // a standalone checkout, not a linked worktree
+	}
+	data, err := os.ReadFile(dot)
+	if err != nil {
+		return false, err
+	}
+	rest, ok := strings.CutPrefix(strings.TrimSpace(string(data)), "gitdir:")
+	if !ok {
+		return false, fmt.Errorf("%s: not a worktree gitdir pointer", dot)
+	}
+	gitDir := strings.TrimSpace(rest)
+	if gitDir == "" {
+		return false, fmt.Errorf("%s: empty gitdir", dot)
+	}
+	if !filepath.IsAbs(gitDir) {
+		gitDir = filepath.Join(path, gitDir)
+	}
+	// The git dir is "<repo>/.git/worktrees/<name>"; both it and the shared .git
+	// it sits in must be absent before the repo counts as gone.
+	for _, dir := range []string{gitDir, filepath.Dir(filepath.Dir(gitDir))} {
+		if _, err := os.Stat(dir); err == nil {
+			return false, nil
+		} else if !os.IsNotExist(err) {
+			return false, err
+		}
+	}
+	return true, nil
+}
+
+// repoFromDirName recovers the repo name from the "<repo>__<branch>" layout used
+// under the worktree root, for entries git can no longer answer for.
+func repoFromDirName(name string) string {
+	if repo, _, ok := strings.Cut(name, "__"); ok {
+		return repo
+	}
+	return name
+}
+
+// allWorktrees is every worktree prune should consider: the managed ones under
+// the worktree root, plus whatever `git worktree list` reports for the repos
+// they belong to and for every checkout in the source root. The second source
+// finds hand-made worktrees and stale registrations whose directory is gone, and
+// carries git's own locked/prunable flags onto the entries the first source
+// already found.
+func allWorktrees() ([]managedWt, error) {
+	managed, err := managedWorktrees()
+	if err != nil {
+		return nil, err
+	}
+	wr, err := worktreeRoot()
+	if err != nil {
+		return nil, err
+	}
+
+	out := make([]managedWt, 0, len(managed))
+	index := map[string]int{}
+	for _, w := range managed {
+		index[resolvePath(w.path)] = len(out)
+		out = append(out, w)
+	}
+
+	for _, srcDir := range sourceRepos(managed) {
+		wts, err := agent.GitWorktreeList(srcDir)
+		if err != nil {
+			continue // not a repo any more, or unreadable; managed entries still stand
+		}
+		for _, wt := range wts {
+			if wt.Bare || sameDir(wt.Path, srcDir) {
+				continue
+			}
+			_, statErr := os.Stat(wt.Path)
+			entry := managedWt{
+				repo:     filepath.Base(srcDir),
+				branch:   worktreeBranch(wt),
+				path:     wt.Path,
+				srcDir:   srcDir,
+				managed:  underRoot(wt.Path, wr),
+				detached: wt.Detached,
+				locked:   wt.Locked,
+				missing:  wt.Prunable != "" || os.IsNotExist(statErr),
+			}
+			key := resolvePath(wt.Path)
+			if i, ok := index[key]; ok {
+				// Keep the managed scan's own view, but adopt the flags only git knows.
+				out[i].locked = entry.locked
+				out[i].missing = out[i].missing || entry.missing
+				out[i].detached = out[i].detached || entry.detached
+				continue
+			}
+			index[key] = len(out)
+			out = append(out, entry)
+		}
+	}
+	sort.Slice(out, func(i, j int) bool {
+		if out[i].repo != out[j].repo {
+			return out[i].repo < out[j].repo
+		}
+		return out[i].path < out[j].path
+	})
+	return out, nil
+}
+
+// resolvePath is a path key that matches however git spells the same directory.
+func resolvePath(path string) string {
+	if p, err := filepath.EvalSymlinks(path); err == nil {
+		return p
+	}
+	return filepath.Clean(path)
+}
+
+// worktreeBranch names a worktree's branch, reporting a detached checkout as
+// "HEAD" so it reads the same as GitCurrentBranch does.
+func worktreeBranch(wt agent.Worktree) string {
+	if wt.Branch != "" {
+		return wt.Branch
+	}
+	return "HEAD"
+}
+
+// sourceRepos is every repo to enumerate worktrees from: the ones the managed
+// worktrees point back at, plus every git checkout directly under the source
+// root (so a repo with only hand-made worktrees is still covered). Each is
+// normalised to its main checkout, because a directory in the source root may
+// itself be a linked worktree — enumerating from there would report the repo's
+// real checkout as a removable worktree of itself.
+func sourceRepos(managed []managedWt) []string {
+	seen := map[string]bool{}
+	var dirs []string
+	add := func(dir string) {
+		if dir == "" {
+			return
+		}
+		if main, err := agent.SourceRepoDir(dir); err == nil {
+			dir = main
+		}
+		key := resolvePath(dir)
+		if seen[key] {
+			return
+		}
+		seen[key] = true
+		dirs = append(dirs, dir)
+	}
+	for _, w := range managed {
+		add(w.srcDir)
+	}
+	if sr, err := srcRoot(); err == nil {
+		if entries, err := os.ReadDir(sr); err == nil {
+			for _, e := range entries {
+				if !e.IsDir() {
+					continue
+				}
+				dir := filepath.Join(sr, e.Name())
+				if _, err := os.Stat(filepath.Join(dir, ".git")); err == nil {
+					add(dir)
+				}
+			}
+		}
+	}
+	sort.Strings(dirs)
+	return dirs
+}
+
+// sameDir compares two paths after resolving symlinks, because git reports
+// worktree paths fully resolved while our own paths may not be.
+func sameDir(a, b string) bool {
+	if a == b {
+		return true
+	}
+	ra, errA := filepath.EvalSymlinks(a)
+	rb, errB := filepath.EvalSymlinks(b)
+	return errA == nil && errB == nil && ra == rb
+}
+
+// underRoot reports whether path sits inside root, comparing resolved paths
+// because git hands back worktree paths with symlinks already resolved.
+func underRoot(path, root string) bool {
+	if r, err := filepath.EvalSymlinks(root); err == nil {
+		root = r
+	}
+	if p, err := filepath.EvalSymlinks(path); err == nil {
+		path = p
+	}
+	rel, err := filepath.Rel(root, path)
+	if err != nil {
+		return false
+	}
+	return rel != ".." && !strings.HasPrefix(rel, ".."+string(filepath.Separator))
+}
+
 // --- rm -------------------------------------------------------------------
 
 func newRmCmd() *cobra.Command {
@@ -312,7 +556,7 @@ func resolveWorktree(target string) (managedWt, error) {
 	}
 	abs, _ := filepath.Abs(target)
 	for _, w := range managed {
-		if w.path == target || w.path == abs || w.branch == target {
+		if w.path == target || w.path == abs || (w.branch != "" && w.branch == target) {
 			return w, nil
 		}
 	}
@@ -323,6 +567,18 @@ func resolveWorktree(target string) (managedWt, error) {
 // forceBranch overrides git's unmerged-branch guard, so only a caller that
 // proved the commits survive elsewhere may set it.
 func removeWorktree(out io.Writer, wt managedWt, deleteBranch, forceBranch bool) error {
+	switch {
+	case wt.inspectErr != nil:
+		// No srcDir to act through and no idea what is in there; --include-keep
+		// must not turn that into a delete.
+		return fmt.Errorf("refusing to remove %s: git state unreadable: %w", wt.path, wt.inspectErr)
+	case wt.orphan:
+		return removeOrphanDir(out, wt)
+	case wt.missing:
+		// The working tree is already gone; only the registration is left.
+		_, _ = fmt.Fprintf(out, "pruned stale registration %s\n", wt.path)
+		return agent.GitWorktreePrune(wt.srcDir)
+	}
 	if err := agent.GitWorktreeRemove(wt.srcDir, wt.path, true); err != nil {
 		return err
 	}
@@ -340,6 +596,24 @@ func removeWorktree(out io.Writer, wt managedWt, deleteBranch, forceBranch bool)
 	return agent.GitWorktreePrune(wt.srcDir)
 }
 
+// removeOrphanDir deletes a worktree directory whose backing repo is gone. git
+// cannot act on it, so this is a plain delete — confined to the worktree root so
+// a bad path can never reach a real checkout.
+func removeOrphanDir(out io.Writer, wt managedWt) error {
+	wr, err := worktreeRoot()
+	if err != nil {
+		return err
+	}
+	if !underRoot(wt.path, wr) || sameDir(wt.path, wr) {
+		return fmt.Errorf("refusing to delete %s: not inside the worktree root %s", wt.path, wr)
+	}
+	if err := os.RemoveAll(wt.path); err != nil {
+		return err
+	}
+	_, _ = fmt.Fprintf(out, "deleted orphaned worktree directory %s\n", wt.path)
+	return nil
+}
+
 // deleteLocalBranch tries the guarded delete first so git refuses to drop
 // unmerged commits on its own; force is a fallback, never the first attempt.
 func deleteLocalBranch(wt managedWt, force bool) error {

cmd/agentws/prune.go

@@ -1,11 +1,15 @@
 package main
 
 import (
+	"encoding/json"
 	"errors"
 	"fmt"
 	"io"
+	"os"
 	"path/filepath"
 	"sort"
+	"strings"
+	"text/tabwriter"
 
 	"git.unkin.net/unkin/agent-tools/internal/agent"
 
@@ -43,22 +47,49 @@ type repoCtx struct {
 	// fetched records that this run's pruning fetch succeeded; without it an
 	// origin/<branch> ref may be stale and due for deletion, so it proves nothing.
 	fetched bool
+	// unfetched explains why, so a verdict can say which it was.
+	unfetched string
+}
+
+// pruneOpts is the knob set runPrune is driven by.
+type pruneOpts struct {
+	apply            bool
+	keepBranches     bool
+	noFetch          bool
+	jsonOut          bool
+	includeKeep      bool
+	includeUnmanaged bool
+}
+
+// reportEntry is the --json shape: one object per worktree, mirroring the table.
+type reportEntry struct {
+	Repo    string `json:"repo"`
+	Branch  string `json:"branch"`
+	Path    string `json:"path"`
+	Verdict string `json:"verdict"`
+	Reason  string `json:"reason"`
+	Managed bool   `json:"managed"`
+	Applied bool   `json:"applied"`
 }
 
 func newPruneCmd() *cobra.Command {
-	var apply, keepBranches bool
+	var opts pruneOpts
 	cmd := &cobra.Command{
 		Use:          "prune",
-		Short:        "Classify managed worktrees and remove the ones whose work is safely upstream",
-		Long:         "prune inspects every managed worktree, classifies it against git and its Gitea\npull request, and removes the ones whose work is provably upstream. It is a dry\nrun unless --yes is given.",
+		Short:        "Classify worktrees and remove the ones whose work is safely upstream",
+		Long:         "prune inspects every worktree it can find — the managed ones under the worktree\nroot plus whatever `git worktree list` reports for the source checkouts — and\nclassifies each against git and its Gitea pull request. It reports and changes\nnothing unless --yes is given.",
 		SilenceUsage: true,
 		RunE: func(cmd *cobra.Command, args []string) error {
-			return runPrune(cmd.OutOrStdout(), pruneClient(), apply, keepBranches)
+			return runPrune(cmd.OutOrStdout(), cmd.ErrOrStderr(), pruneClient(), opts)
 		},
 	}
 	f := cmd.Flags()
-	f.BoolVar(&apply, "yes", false, "Actually remove worktrees (default is a dry run)")
-	f.BoolVar(&keepBranches, "keep-branches", false, "Never delete a local branch, whatever the classification")
+	f.BoolVar(&opts.apply, "yes", false, "Actually remove worktrees (default is a dry run)")
+	f.BoolVar(&opts.keepBranches, "keep-branches", false, "Never delete a local branch, whatever the classification")
+	f.BoolVar(&opts.noFetch, "no-fetch", false, "Do not fetch; judge against the refs already on disk")
+	f.BoolVar(&opts.jsonOut, "json", false, "Emit JSON instead of a table")
+	f.BoolVar(&opts.includeKeep, "include-keep", false, "Dangerous: also remove worktrees classified keep (needs --yes). Destroys uncommitted changes and paused rebase/merge state, which no branch is carrying; only the branch itself survives")
+	f.BoolVar(&opts.includeUnmanaged, "include-unmanaged", false, "Also remove worktrees that live outside the worktree root")
 	return cmd
 }
 
@@ -72,58 +103,153 @@ func pruneClient() prLister {
 	return agent.NewGiteaClient(tok)
 }
 
-func runPrune(out io.Writer, prs prLister, apply, keepBranches bool) error {
-	managed, err := managedWorktrees()
+func runPrune(out, errOut io.Writer, prs prLister, opts pruneOpts) error {
+	// In JSON mode stdout carries the document alone, so notes go to stderr.
+	notes := out
+	if opts.jsonOut {
+		notes = errOut
+	}
+
+	worktrees, err := allWorktrees()
 	if err != nil {
 		return err
 	}
-	if len(managed) == 0 {
+	if len(worktrees) == 0 {
+		if opts.jsonOut {
+			_, _ = fmt.Fprintln(out, "[]")
+			return nil
+		}
 		_, _ = fmt.Fprintln(out, "no managed worktrees")
 		return nil
 	}
 
-	byRepo := map[string][]managedWt{}
-	for _, w := range managed {
-		byRepo[w.srcDir] = append(byRepo[w.srcDir], w)
+	results := classifyAll(notes, prs, worktrees, opts)
+	if err := report(out, results, opts); err != nil {
+		return err
 	}
+	if !opts.apply {
+		if !opts.jsonOut {
+			_, _ = fmt.Fprintln(out, "dry run: nothing removed (pass --yes to apply)")
+		}
+		return nil
+	}
+	return applyPrune(notes, results, opts)
+}
+
+// classifyAll groups worktrees by source repo so each repo is fetched and its
+// PRs listed once, then classifies every worktree against that repo's state.
+func classifyAll(notes io.Writer, prs prLister, worktrees []managedWt, opts pruneOpts) []pruneResult {
+	byRepo := map[string][]managedWt{}
+	var results []pruneResult
+	for _, w := range worktrees {
+		switch {
+		case w.inspectErr != nil:
+			// Unknown is not gone: a checkout git refused to answer for keeps.
+			results = append(results, pruneResult{wt: w, verdict: verdictKeep, reason: "inspection failed: " + oneLine(w.inspectErr.Error())})
+		case w.orphan:
+			results = append(results, pruneResult{wt: w, verdict: verdictRemove, reason: "backing repo gone, no git state to read"})
+		default:
+			byRepo[w.srcDir] = append(byRepo[w.srcDir], w)
+		}
+	}
+
 	srcDirs := make([]string, 0, len(byRepo))
 	for dir := range byRepo {
 		srcDirs = append(srcDirs, dir)
 	}
 	sort.Strings(srcDirs)
 
-	var results []pruneResult
 	for _, srcDir := range srcDirs {
-		ctx, err := newRepoCtx(out, prs, srcDir)
+		ctx, err := newRepoCtx(notes, prs, srcDir, opts.noFetch)
 		if err != nil {
 			for _, w := range byRepo[srcDir] {
-				results = append(results, pruneResult{wt: w, verdict: verdictKeep, reason: "repo state unknown: " + err.Error()})
+				results = append(results, pruneResult{wt: w, verdict: verdictKeep, reason: "repo state unknown: " + oneLine(err.Error())})
 			}
 			continue
 		}
 		for _, w := range byRepo[srcDir] {
 			res, err := classify(w, ctx)
 			if err != nil {
-				res = pruneResult{wt: w, verdict: verdictKeep, reason: "inspection failed: " + err.Error()}
+				res = pruneResult{wt: w, verdict: verdictKeep, reason: "inspection failed: " + oneLine(err.Error())}
 			}
 			results = append(results, res)
 		}
 	}
+	sort.SliceStable(results, func(i, j int) bool {
+		if results[i].wt.repo != results[j].wt.repo {
+			return results[i].wt.repo < results[j].wt.repo
+		}
+		return results[i].wt.path < results[j].wt.path
+	})
+	return results
+}
 
+// report writes the classification as a table or as JSON.
+func report(out io.Writer, results []pruneResult, opts pruneOpts) error {
+	if opts.jsonOut {
+		entries := make([]reportEntry, 0, len(results))
+		for _, r := range results {
+			entries = append(entries, reportEntry{
+				Repo:    r.wt.repo,
+				Branch:  r.wt.branch,
+				Path:    r.wt.path,
+				Verdict: plannedVerdict(r, opts),
+				Reason:  r.reason,
+				Managed: r.wt.managed,
+				Applied: opts.apply && willRemove(r, opts),
+			})
+		}
+		enc := json.NewEncoder(out)
+		enc.SetIndent("", "  ")
+		return enc.Encode(entries)
+	}
+
+	// Padded with spaces only, so the table reads the same with or without a TTY.
+	tw := tabwriter.NewWriter(out, 0, 0, 2, ' ', 0)
+	_, _ = fmt.Fprintln(tw, "REPO\tBRANCH\tPATH\tVERDICT\tREASON")
 	for _, r := range results {
-		_, _ = fmt.Fprintf(out, "%-44s %-34s %-14s %s\n", filepath.Base(r.wt.path), r.wt.branch, plannedVerdict(r, keepBranches), r.reason)
-	}
-	if !apply {
-		_, _ = fmt.Fprintln(out, "dry run: nothing removed (pass --yes to apply)")
-		return nil
+		_, _ = fmt.Fprintf(tw, "%s\t%s\t%s\t%s\t%s\n",
+			dash(r.wt.repo), dash(r.wt.branch), abbrevHome(r.wt.path), plannedVerdict(r, opts), r.reason)
 	}
+	return tw.Flush()
+}
 
+// oneLine flattens a git error onto a single line so one row stays one row.
+func oneLine(s string) string {
+	return strings.Join(strings.Fields(s), " ")
+}
+
+func dash(s string) string {
+	if s == "" {
+		return "-"
+	}
+	return s
+}
+
+// abbrevHome shortens $HOME to ~ so paths do not dominate the table.
+func abbrevHome(path string) string {
+	home, err := os.UserHomeDir()
+	if err != nil || home == "" || !strings.HasPrefix(path, home+string(filepath.Separator)) {
+		return path
+	}
+	return "~" + path[len(home):]
+}
+
+// applyPrune performs the removals the classification authorised, reporting each
+// one and collecting failures so one bad worktree does not stop the rest.
+func applyPrune(out io.Writer, results []pruneResult, opts pruneOpts) error {
 	var errs []error
 	for _, r := range results {
-		if r.verdict == verdictKeep {
+		if !willRemove(r, opts) {
+			if !r.wt.managed && r.verdict != verdictKeep {
+				_, _ = fmt.Fprintf(out, "skipped %s: outside the worktree root (pass --include-unmanaged)\n", r.wt.path)
+			}
 			continue
 		}
-		deleteBranch := r.verdict == verdictRemoveBranch && !keepBranches
+		if r.verdict == verdictKeep {
+			_, _ = fmt.Fprintf(out, "warn: removing %s despite %q (--include-keep)\n", r.wt.path, r.reason)
+		}
+		deleteBranch := plannedVerdict(r, opts) == verdictRemoveBranch
 		if err := removeWorktree(out, r.wt, deleteBranch, r.proven); err != nil {
 			errs = append(errs, fmt.Errorf("%s: %w", r.wt.path, err))
 		}
@@ -131,23 +257,44 @@ func runPrune(out io.Writer, prs prLister, apply, keepBranches bool) error {
 	return errors.Join(errs...)
 }
 
-// plannedVerdict is what will actually happen, so --keep-branches does not
-// print a branch deletion it will not perform.
-func plannedVerdict(r pruneResult, keepBranches bool) string {
-	if keepBranches && r.verdict == verdictRemoveBranch {
+// willRemove is the single gate on destruction: a keep verdict needs
+// --include-keep, and a worktree outside the worktree root needs
+// --include-unmanaged.
+func willRemove(r pruneResult, opts pruneOpts) bool {
+	if !r.wt.managed && !opts.includeUnmanaged {
+		return false
+	}
+	if r.verdict == verdictKeep {
+		return opts.includeKeep
+	}
+	return true
+}
+
+// plannedVerdict is what will actually happen, so no flag prints an action it
+// will not perform. A detached HEAD has no branch to delete, and a keep forced
+// through with --include-keep never takes its branch with it.
+func plannedVerdict(r pruneResult, opts pruneOpts) string {
+	if r.verdict != verdictRemoveBranch {
+		return r.verdict
+	}
+	if opts.keepBranches || r.wt.detached {
 		return verdictRemove
 	}
-	return r.verdict
+	return verdictRemoveBranch
 }
 
 // newRepoCtx refreshes a source repo and collects the signals prune classifies
-// against. A failed fetch or an unreachable Gitea is reported and tolerated:
-// the signals that hold offline still work, and the rest are recorded as
-// unverified.
-func newRepoCtx(out io.Writer, prs prLister, srcDir string) (repoCtx, error) {
+// against. A failed or skipped fetch and an unreachable Gitea are reported and
+// tolerated: the signals that hold offline still work, and the rest are recorded
+// as unverified.
+func newRepoCtx(out io.Writer, prs prLister, srcDir string, noFetch bool) (repoCtx, error) {
 	ctx := repoCtx{srcDir: srcDir, prs: map[string]agent.PullRequest{}}
 	repo := filepath.Base(srcDir)
-	if err := agent.GitFetchPrune(srcDir, "origin", credentialHelperArgs()...); err != nil {
+	if noFetch {
+		ctx.unfetched = "fetch skipped"
+		_, _ = fmt.Fprintf(out, "warn: fetch %s skipped (--no-fetch, remote state unverified)\n", repo)
+	} else if err := agent.GitFetchPrune(srcDir, "origin", credentialHelperArgs()...); err != nil {
+		ctx.unfetched = "fetch failed"
 		_, _ = fmt.Fprintf(out, "warn: fetch %s: %v (remote state unverified)\n", repo, err)
 	} else {
 		ctx.fetched = true
@@ -225,14 +372,33 @@ func headContainedIn(dir, ref string) bool {
 	return err == nil && ok
 }
 
-// classify applies the prune precedence: dirty and open-PR worktrees are kept,
-// provably-upstream work loses its branch too, and anything unproven keeps its
-// branch so no commits become unreachable. A PR's state alone never authorises
-// deleting a branch — git must confirm HEAD is contained in what merged or in
-// what origin still holds, and origin's refs only count when this run's pruning
-// fetch refreshed them.
+// classify applies the prune precedence. Removal must never destroy state that
+// exists nowhere else: a vanished working tree is the one case with nothing to
+// lose, a locked or mid-rebase checkout holds sequencer state git itself refuses
+// to discard, and a dirty checkout or a detached HEAD with unique commits holds
+// work no branch is carrying. Past those guards, provably-upstream work loses its
+// branch too, and anything unproven keeps its branch so no commit becomes
+// unreachable. A PR's state alone never authorises deleting a branch — git must
+// confirm HEAD is contained in what merged or in what origin still holds, and
+// origin's refs only count when this run's pruning fetch refreshed them.
 func classify(wt managedWt, ctx repoCtx) (pruneResult, error) {
 	res := pruneResult{wt: wt}
+	if wt.missing {
+		res.verdict, res.reason = verdictRemove, "working tree gone, stale registration only"
+		return res, nil
+	}
+	if wt.locked {
+		res.verdict, res.reason = verdictKeep, "locked"
+		return res, nil
+	}
+	op, err := agent.GitInProgressOp(wt.path)
+	if err != nil {
+		return res, err
+	}
+	if op != "" {
+		res.verdict, res.reason = verdictKeep, op+" in progress"
+		return res, nil
+	}
 	dirty, err := agent.GitIsDirty(wt.path)
 	if err != nil {
 		return res, err
@@ -267,6 +433,15 @@ func classify(wt managedWt, ctx repoCtx) (pruneResult, error) {
 		return res, nil
 	}
 
+	local, err := agent.GitCommitsNotOnRemotes(wt.path)
+	if err != nil {
+		return res, err
+	}
+	if wt.detached && local > 0 {
+		res.verdict, res.reason = verdictKeep, fmt.Sprintf("detached HEAD carrying %s on no remote", commitCount(local))
+		return res, nil
+	}
+
 	remote := "origin/" + wt.branch
 	onOrigin := hasPR && ctx.fetched && agent.GitRemoteBranchExists(ctx.srcDir, "origin", wt.branch)
 	switch {
@@ -275,7 +450,7 @@ func classify(wt managedWt, ctx repoCtx) (pruneResult, error) {
 	case hasPR && pr.Merged && onOrigin && headContainedIn(wt.path, remote):
 		res.verdict, res.reason, res.proven = verdictRemoveBranch, fmt.Sprintf("PR merged #%d, HEAD contained in %s", pr.Number, remote), true
 	case hasPR && pr.Merged && !ctx.fetched:
-		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR merged #%d, fetch failed so %s is unverified", pr.Number, remote)
+		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR merged #%d, %s so %s is unverified", pr.Number, ctx.unfetched, remote)
 	case hasPR && pr.Merged:
 		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR merged #%d, local commits not in the merged head", pr.Number)
 	case hasPR && onOrigin && headContainedIn(wt.path, remote):
@@ -283,7 +458,7 @@ func classify(wt managedWt, ctx repoCtx) (pruneResult, error) {
 	case hasPR && onOrigin:
 		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR closed #%d, local commits not on %s", pr.Number, remote)
 	case hasPR && !ctx.fetched:
-		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR closed #%d, fetch failed so %s is unverified", pr.Number, remote)
+		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR closed #%d, %s so %s is unverified", pr.Number, ctx.unfetched, remote)
 	case hasPR:
 		res.verdict, res.reason = verdictRemove, fmt.Sprintf("PR closed #%d, branch gone", pr.Number)
 	case ctx.prsKnown:
@@ -291,5 +466,15 @@ func classify(wt managedWt, ctx repoCtx) (pruneResult, error) {
 	default:
 		res.verdict, res.reason = verdictRemove, "PR state unknown"
 	}
+	if res.verdict == verdictRemove && local > 0 {
+		res.reason += fmt.Sprintf(", %s on no remote so branch %s is kept", commitCount(local), wt.branch)
+	}
 	return res, nil
 }
+
+func commitCount(n int) string {
+	if n == 1 {
+		return "1 commit"
+	}
+	return fmt.Sprintf("%d commits", n)
+}

cmd/agentws/prune_test.go

@@ -166,17 +166,22 @@ func closedPR(number int, branch string) map[string]any {
 
 func run(t *testing.T, prs prLister, apply, keepBranches bool) string {
 	t.Helper()
-	var out bytes.Buffer
-	if err := runPrune(&out, prs, apply, keepBranches); err != nil {
-		t.Fatalf("runPrune: %v\n%s", err, out.String())
+	return runOpts(t, prs, pruneOpts{apply: apply, keepBranches: keepBranches})
+}
+
+func runOpts(t *testing.T, prs prLister, opts pruneOpts) string {
+	t.Helper()
+	var out, errOut bytes.Buffer
+	if err := runPrune(&out, &errOut, prs, opts); err != nil {
+		t.Fatalf("runPrune: %v\n%s%s", err, out.String(), errOut.String())
 	}
-	return out.String()
+	return out.String() + errOut.String()
 }
 
 func lineFor(t *testing.T, out, branch string) string {
 	t.Helper()
 	for _, line := range strings.Split(out, "\n") {
-		if strings.Contains(line, " "+branch+" ") {
+		if fields := strings.Fields(line); len(fields) > 1 && fields[1] == branch {
 			return line
 		}
 	}
@@ -184,11 +189,12 @@ func lineFor(t *testing.T, out, branch string) string {
 	return ""
 }
 
+// assertVerdict reads the table row for a branch: REPO BRANCH PATH VERDICT REASON.
 func assertVerdict(t *testing.T, out, branch, verdict, reason string) {
 	t.Helper()
 	line := lineFor(t, out, branch)
 	fields := strings.Fields(line)
-	if len(fields) < 3 || fields[2] != verdict {
+	if len(fields) < 4 || fields[3] != verdict {
 		t.Errorf("branch %s: verdict line %q, want verdict %q", branch, line, verdict)
 	}
 	if reason != "" && !strings.Contains(line, reason) {
@@ -559,12 +565,12 @@ func (f *fixture) breakRemote(t *testing.T) {
 // classification and the removals it authorised happen regardless.
 func applyUnreachable(t *testing.T, prs prLister) string {
 	t.Helper()
-	var out bytes.Buffer
-	err := runPrune(&out, prs, true, false)
+	var out, errOut bytes.Buffer
+	err := runPrune(&out, &errOut, prs, pruneOpts{apply: true})
 	if err == nil {
 		t.Fatalf("expected the refresh fetch to fail against a missing remote:\n%s", out.String())
 	}
-	return out.String()
+	return out.String() + errOut.String()
 }
 
 // staleFixture builds a repo where origin/<branch> covers HEAD for a closed and
@@ -685,3 +691,433 @@ func TestRepoPathFollowsOrigin(t *testing.T) {
 		t.Errorf("repoPath for a local remote = %q, want unkin/dotfiles", got)
 	}
 }
+
+// --- discovery beyond the worktree root -----------------------------------
+
+// gitAllow runs git and returns its combined output without failing the test,
+// for commands that are expected to stop mid-way (e.g. an interrupted rebase).
+func gitAllow(t *testing.T, dir string, args ...string) string {
+	t.Helper()
+	cmd := exec.Command("git", args...)
+	cmd.Dir = dir
+	out, _ := cmd.CombinedOutput()
+	return strings.TrimSpace(string(out))
+}
+
+// addManualWorktree creates a worktree outside the worktree root, the way a
+// person would by hand, so only `git worktree list` can find it.
+func (f *fixture) addManualWorktree(t *testing.T, branch string) string {
+	t.Helper()
+	path := filepath.Join(f.root, "manual", agent.SanitizeBranch(branch))
+	git(t, f.srcDir, "worktree", "add", path, "-b", branch, "origin/main")
+	identity(t, path)
+	return path
+}
+
+// A hand-made worktree outside the worktree root is still classified, but the
+// default run refuses to remove it: that needs --include-unmanaged.
+func TestPruneReportsUnmanagedWorktreeButKeepsIt(t *testing.T) {
+	f := newFixture(t)
+	manual := f.addManualWorktree(t, "benvin/by-hand")
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "benvin/by-hand", verdictRemoveBranch, "contained in origin/main")
+	if !strings.Contains(out, "--include-unmanaged") {
+		t.Errorf("output should name the flag that would remove it:\n%s", out)
+	}
+	if !exists(manual) {
+		t.Error("an unmanaged worktree must survive without --include-unmanaged")
+	}
+	if !agent.GitBranchExists(f.srcDir, "benvin/by-hand") {
+		t.Error("an unmanaged worktree's branch must survive too")
+	}
+}
+
+func TestPruneRemovesUnmanagedWorktreeWithFlag(t *testing.T) {
+	f := newFixture(t)
+	manual := f.addManualWorktree(t, "benvin/by-hand")
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true, includeUnmanaged: true})
+	assertVerdict(t, out, "benvin/by-hand", verdictRemoveBranch, "contained in origin/main")
+	if exists(manual) {
+		t.Error("--include-unmanaged should have removed the worktree")
+	}
+}
+
+// --include-unmanaged only lifts the location gate. A keep verdict is a separate
+// gate, so a dirty hand-made worktree still needs --include-keep to be touched.
+func TestPruneIncludeUnmanagedStillObeysKeep(t *testing.T) {
+	f := newFixture(t)
+	manual := f.addManualWorktree(t, "benvin/by-hand")
+	if err := os.WriteFile(filepath.Join(manual, "scratch.txt"), []byte("wip\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true, includeUnmanaged: true})
+	assertVerdict(t, out, "benvin/by-hand", verdictKeep, "dirty")
+	if !exists(filepath.Join(manual, "scratch.txt")) {
+		t.Error("--include-unmanaged must not remove a worktree classified keep")
+	}
+}
+
+// A worktree whose directory was deleted leaves only a registration behind:
+// there is nothing to lose, so it is prunable outright.
+func TestPruneStaleRegistrationWithMissingDirectory(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/vanished")
+	writeCommit(t, wt, "v.txt", "v\n", "work")
+	if err := os.RemoveAll(wt); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "benvin/vanished", verdictRemove, "working tree gone")
+
+	wts, err := agent.GitWorktreeList(f.srcDir)
+	if err != nil {
+		t.Fatal(err)
+	}
+	for _, w := range wts {
+		if w.Path == wt {
+			t.Errorf("registration for %s should have been pruned: %+v", wt, w)
+		}
+	}
+	if !agent.GitBranchExists(f.srcDir, "benvin/vanished") {
+		t.Error("pruning a registration must not delete the branch")
+	}
+}
+
+// A directory under the worktree root whose backing repo is gone cannot be
+// inspected by git at all, so prune deletes the leftover directory.
+func TestPruneOrphanedDirectoryWhenRepoIsGone(t *testing.T) {
+	f := newFixture(t)
+	other := filepath.Join(f.root, "src", "other")
+	git(t, filepath.Join(f.root, "src"), "clone", f.bare, other)
+	identity(t, other)
+	orphan := filepath.Join(f.wtRoot, agent.WorktreeDirName("other", "benvin/orphaned"))
+	git(t, other, "worktree", "add", orphan, "-b", "benvin/orphaned", "origin/main")
+	if err := os.RemoveAll(other); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "-", verdictRemove, "backing repo gone")
+	if exists(orphan) {
+		t.Error("an orphaned worktree directory should have been deleted")
+	}
+}
+
+// addForeignWorktree clones a second repo under the source root and gives it a
+// worktree under the worktree root, so it can be broken without touching the
+// fixture's own repo. It returns the clone and the worktree path.
+func (f *fixture) addForeignWorktree(t *testing.T, repo, branch string) (string, string) {
+	t.Helper()
+	src := filepath.Join(f.root, "src", repo)
+	git(t, filepath.Join(f.root, "src"), "clone", f.bare, src)
+	identity(t, src)
+	wt := filepath.Join(f.wtRoot, agent.WorktreeDirName(repo, branch))
+	git(t, src, "worktree", "add", wt, "-b", branch, "origin/main")
+	return src, wt
+}
+
+// The regression this guards: git failing for a reason that is not "the backing
+// repo is gone" used to be read as orphan, and orphan deletes the directory
+// outright. Here the git dir is still on disk — only its commondir pointer is
+// broken, as a half-written or momentarily unreachable repo would be — so the
+// verdict must be keep and the directory must survive a --yes run.
+func TestPruneKeepsWorktreeWhenGitFailsButRepoExists(t *testing.T) {
+	f := newFixture(t)
+	src, wt := f.addForeignWorktree(t, "other", "benvin/unreadable")
+	writeCommit(t, wt, "u.txt", "u\n", "work")
+	gitDir, err := agent.GitDir(wt)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if err := os.Remove(filepath.Join(gitDir, "commondir")); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := agent.GitCurrentBranch(wt); err == nil {
+		t.Fatal("fixture did not break git in the worktree")
+	}
+	if !exists(gitDir) || !exists(filepath.Join(src, ".git")) {
+		t.Fatal("fixture removed the backing repo; it must still be present")
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "-", verdictKeep, "inspection failed")
+	if !exists(wt) {
+		t.Error("a worktree git could not be read must not be deleted")
+	}
+}
+
+// The same rule one step further in: the registration is gone but the repo is
+// not, so the directory is still recoverable and must not be deleted.
+func TestPruneKeepsWorktreeWhenOnlyRegistrationIsGone(t *testing.T) {
+	f := newFixture(t)
+	src, wt := f.addForeignWorktree(t, "other", "benvin/deregistered")
+	gitDir, err := agent.GitDir(wt)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if err := os.RemoveAll(gitDir); err != nil {
+		t.Fatal(err)
+	}
+	if !exists(filepath.Join(src, ".git")) {
+		t.Fatal("fixture removed the backing repo; it must still be present")
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "-", verdictKeep, "inspection failed")
+	if !exists(wt) {
+		t.Error("a worktree whose repo still exists must not be deleted")
+	}
+}
+
+// --include-keep overrides a keep, but it must not become a second route to the
+// deletion finding #1 closed: with no readable git state there is nothing to
+// remove through, so the removal fails loudly and the directory stays.
+func TestPruneIncludeKeepDoesNotDeleteUnreadableWorktree(t *testing.T) {
+	f := newFixture(t)
+	_, wt := f.addForeignWorktree(t, "other", "benvin/forced")
+	gitDir, err := agent.GitDir(wt)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if err := os.Remove(filepath.Join(gitDir, "commondir")); err != nil {
+		t.Fatal(err)
+	}
+
+	var out, errOut bytes.Buffer
+	err = runPrune(&out, &errOut, client(fakeGitea(t)), pruneOpts{apply: true, includeKeep: true})
+	if err == nil {
+		t.Error("forcing removal of an unreadable worktree should fail, not succeed silently")
+	}
+	if !exists(wt) {
+		t.Error("--include-keep must not delete a worktree whose git state is unknown")
+	}
+}
+
+// --- safety signals -------------------------------------------------------
+
+// An interrupted rebase holds sequencer state that exists nowhere else, and it
+// detaches HEAD while it runs, so it must outrank every other signal.
+func TestPruneKeepsInterruptedRebase(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/rebasing")
+	writeCommit(t, wt, "r.txt", "r\n", "work")
+	gitAllow(t, wt, "rebase", "--exec", "false", "origin/main")
+	if op, err := agent.GitInProgressOp(wt); err != nil || op != "rebase" {
+		t.Fatalf("fixture did not leave a rebase in progress: op=%q err=%v", op, err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "HEAD", verdictKeep, "rebase in progress")
+	if !exists(wt) {
+		t.Error("a worktree mid-rebase must not be removed")
+	}
+}
+
+// A half-finished cherry-pick is the same case with a branch still checked out,
+// so the sequencer check has to run before the dirty check can mask it.
+func TestPruneKeepsInterruptedCherryPick(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/picking")
+	gitDir, err := agent.GitDir(wt)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(gitDir, "CHERRY_PICK_HEAD"), []byte(git(t, wt, "rev-parse", "HEAD")+"\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "benvin/picking", verdictKeep, "cherry-pick in progress")
+	if !exists(wt) {
+		t.Error("a worktree mid-cherry-pick must not be removed")
+	}
+}
+
+// A detached HEAD has no branch to carry its commits, so unique work there is
+// unrecoverable once the worktree goes.
+func TestPruneKeepsDetachedHeadWithUniqueCommits(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/detaching")
+	writeCommit(t, wt, "d.txt", "d\n", "work")
+	git(t, wt, "checkout", "--detach")
+	git(t, f.srcDir, "branch", "-D", "benvin/detaching")
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "HEAD", verdictKeep, "detached HEAD carrying 1 commit on no remote")
+	if !exists(wt) {
+		t.Error("a detached worktree with unique commits must not be removed")
+	}
+}
+
+// A detached HEAD whose commit is already upstream is safe to drop, but there is
+// no branch to delete, so the verdict must not promise one.
+func TestPruneDetachedHeadContainedUpstream(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/detached-clean")
+	git(t, wt, "checkout", "--detach")
+	git(t, f.srcDir, "branch", "-D", "benvin/detached-clean")
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "HEAD", verdictRemove, "contained in origin/main")
+	if strings.Contains(out, verdictRemoveBranch) {
+		t.Errorf("a detached worktree has no branch to delete:\n%s", out)
+	}
+	if exists(wt) {
+		t.Error("a detached worktree contained upstream should have been removed")
+	}
+}
+
+// git refuses to drop a locked worktree, and so does prune.
+func TestPruneKeepsLockedWorktree(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/locked")
+	git(t, f.srcDir, "worktree", "lock", wt)
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true})
+	assertVerdict(t, out, "benvin/locked", verdictKeep, "locked")
+	if !exists(wt) {
+		t.Error("a locked worktree must not be removed")
+	}
+}
+
+// Unproven work is only safe to abandon because the branch keeps it, so the
+// reason has to say so rather than leaving the operator to guess.
+func TestPruneReasonNamesRetainedBranch(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/unpushed")
+	writeCommit(t, wt, "u.txt", "u\n", "work")
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{})
+	assertVerdict(t, out, "benvin/unpushed", verdictRemove, "1 commit on no remote so branch benvin/unpushed is kept")
+	if !exists(wt) {
+		t.Error("a dry run must not remove anything")
+	}
+}
+
+// --- flags ----------------------------------------------------------------
+
+// --include-keep is the only way past a keep verdict, and even then the branch
+// stays, so the commits survive the worktree.
+func TestPruneIncludeKeepRemovesDirtyWorktreeButNotItsBranch(t *testing.T) {
+	f := newFixture(t)
+	wt := f.addWorktree(t, "benvin/dirty")
+	writeCommit(t, wt, "d.txt", "d\n", "work")
+	if err := os.WriteFile(filepath.Join(wt, "wip.txt"), []byte("wip\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{apply: true, includeKeep: true})
+	assertVerdict(t, out, "benvin/dirty", verdictKeep, "dirty")
+	if !strings.Contains(out, "--include-keep") {
+		t.Errorf("forcing a keep should warn it is doing so:\n%s", out)
+	}
+	if exists(wt) {
+		t.Error("--include-keep should have removed the dirty worktree")
+	}
+	if !agent.GitBranchExists(f.srcDir, "benvin/dirty") {
+		t.Error("--include-keep must never delete a branch")
+	}
+}
+
+// --no-fetch means origin's refs are whatever is already on disk, so a tracking
+// ref cannot prove the work survives: the branch is kept.
+func TestPruneNoFetchDistrustsTrackingRefs(t *testing.T) {
+	f, srv, closed, _ := staleFixture(t, true)
+
+	out := runOpts(t, client(srv), pruneOpts{apply: true, noFetch: true})
+	if !strings.Contains(out, "--no-fetch") {
+		t.Errorf("output should record that the fetch was skipped:\n%s", out)
+	}
+	assertVerdict(t, out, "benvin/stale-closed", verdictRemove, "is unverified")
+	if exists(closed) {
+		t.Error("worktree should have been removed")
+	}
+	if !agent.GitBranchExists(f.srcDir, "benvin/stale-closed") {
+		t.Error("an unverified tracking ref must not authorise deleting the branch")
+	}
+}
+
+// --json puts the machine-readable document on stdout alone, with the same
+// verdicts the table shows.
+func TestPruneJSONOutput(t *testing.T) {
+	f := newFixture(t)
+	contained := f.addWorktree(t, "benvin/contained")
+	dirty := f.addWorktree(t, "benvin/dirty")
+	if err := os.WriteFile(filepath.Join(dirty, "wip.txt"), []byte("wip\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	srv := fakeGitea(t)
+	var out, errOut bytes.Buffer
+	if err := runPrune(&out, &errOut, client(srv), pruneOpts{jsonOut: true}); err != nil {
+		t.Fatalf("runPrune: %v", err)
+	}
+	var entries []reportEntry
+	if err := json.Unmarshal(out.Bytes(), &entries); err != nil {
+		t.Fatalf("stdout is not JSON (%v): %s", err, out.String())
+	}
+	byBranch := map[string]reportEntry{}
+	for _, e := range entries {
+		byBranch[e.Branch] = e
+	}
+	if got := byBranch["benvin/contained"]; got.Verdict != verdictRemoveBranch || got.Path != contained || !got.Managed || got.Applied {
+		t.Errorf("contained entry = %+v", got)
+	}
+	if got := byBranch["benvin/dirty"]; got.Verdict != verdictKeep || got.Reason != "dirty" {
+		t.Errorf("dirty entry = %+v", got)
+	}
+	if !exists(contained) {
+		t.Error("a --json dry run must not remove anything")
+	}
+	_ = f
+}
+
+// A directory in the source root can itself be a linked worktree. Enumerating
+// from there lists the repo's real checkout, which must never be offered up for
+// removal — discovery normalises each candidate to its main checkout instead.
+func TestPruneNeverOffersAMainCheckout(t *testing.T) {
+	f := newFixture(t)
+	sibling := filepath.Join(f.root, "src", "repo-sibling")
+	git(t, f.srcDir, "worktree", "add", sibling, "-b", "benvin/sibling", "origin/main")
+	identity(t, sibling)
+
+	srv := fakeGitea(t)
+	out := runOpts(t, client(srv), pruneOpts{})
+	for _, line := range strings.Split(out, "\n") {
+		if fields := strings.Fields(line); len(fields) > 2 && fields[2] == f.srcDir {
+			t.Errorf("main checkout %s must not be classified: %q", f.srcDir, line)
+		}
+	}
+	assertVerdict(t, out, "benvin/sibling", verdictRemoveBranch, "contained in origin/main")
+	if strings.Contains(out, "\tmain\t") || lineForBranch(out, "main") != "" {
+		t.Errorf("the default branch's own checkout must not appear:\n%s", out)
+	}
+}
+
+// lineForBranch is lineFor without the fatal, for asserting a row is absent.
+func lineForBranch(out, branch string) string {
+	for _, line := range strings.Split(out, "\n") {
+		if fields := strings.Fields(line); len(fields) > 1 && fields[1] == branch {
+			return line
+		}
+	}
+	return ""
+}

internal/agent/git.go

@@ -7,6 +7,7 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
+	"strconv"
 	"strings"
 )
 
@@ -25,6 +26,10 @@ type Worktree struct {
 	Branch   string // short branch name ("" when detached or bare)
 	Bare     bool
 	Detached bool
+	Locked   bool
+	// Prunable is git's own reason a registration is stale (e.g. "gitdir file
+	// points to non-existent location"); empty when the worktree is intact.
+	Prunable string
 }
 
 // runGit runs git with args, using dir as the working directory (empty = the
@@ -114,6 +119,54 @@ func GitIsDirty(dir string) (bool, error) {
 	return strings.TrimSpace(out) != "", nil
 }
 
+// GitDir returns the absolute path to the git directory backing the checkout at
+// dir (per-worktree, unlike GitCommonDir).
+func GitDir(dir string) (string, error) {
+	return runGit(dir, "rev-parse", "--path-format=absolute", "--git-dir")
+}
+
+// inProgressMarkers maps a sentinel inside the git dir to the operation it means
+// is half-finished. Such a checkout holds state that lives nowhere else.
+var inProgressMarkers = []struct{ path, op string }{
+	{"rebase-merge", "rebase"},
+	{"rebase-apply", "rebase"},
+	{"MERGE_HEAD", "merge"},
+	{"CHERRY_PICK_HEAD", "cherry-pick"},
+	{"REVERT_HEAD", "revert"},
+	{"BISECT_LOG", "bisect"},
+}
+
+// GitInProgressOp names the sequencer operation underway in the checkout at dir,
+// or "" when none is.
+func GitInProgressOp(dir string) (string, error) {
+	gitDir, err := GitDir(dir)
+	if err != nil {
+		return "", err
+	}
+	for _, m := range inProgressMarkers {
+		if _, err := os.Stat(filepath.Join(gitDir, m.path)); err == nil {
+			return m.op, nil
+		} else if !os.IsNotExist(err) {
+			return "", err
+		}
+	}
+	return "", nil
+}
+
+// GitCommitsNotOnRemotes counts commits reachable from HEAD that no
+// remote-tracking ref holds, i.e. work that exists only in this checkout.
+func GitCommitsNotOnRemotes(dir string) (int, error) {
+	out, err := runGit(dir, "rev-list", "--count", "HEAD", "--not", "--remotes")
+	if err != nil {
+		return 0, err
+	}
+	n, err := strconv.Atoi(strings.TrimSpace(out))
+	if err != nil {
+		return 0, fmt.Errorf("parse rev-list count %q: %w", out, err)
+	}
+	return n, nil
+}
+
 // GitIsAncestor reports whether ancestor is reachable from descendant.
 func GitIsAncestor(repoDir, ancestor, descendant string) (bool, error) {
 	cmd := exec.Command("git", "merge-base", "--is-ancestor", ancestor, descendant)
@@ -277,6 +330,18 @@ func ParseWorktreeList(out string) []Worktree {
 			if cur != nil {
 				cur.Detached = true
 			}
+		case "locked":
+			if cur != nil {
+				cur.Locked = true
+			}
+		case "prunable":
+			if cur != nil {
+				// git omits the reason when it has none, so record the flag itself.
+				cur.Prunable = val
+				if cur.Prunable == "" {
+					cur.Prunable = "prunable"
+				}
+			}
 		}
 	}
 	flush()

internal/agent/git_test.go

@@ -42,10 +42,20 @@ branch refs/heads/benvin/foo
 worktree /home/ben/.cache/agentws/repo__detached
 HEAD 3333333333333333333333333333333333333333
 detached
+
+worktree /home/ben/.cache/agentws/repo__gone
+HEAD 4444444444444444444444444444444444444444
+branch refs/heads/benvin/gone
+prunable gitdir file points to non-existent location
+
+worktree /home/ben/.cache/agentws/repo__held
+HEAD 5555555555555555555555555555555555555555
+branch refs/heads/benvin/held
+locked
 `
 	wts := ParseWorktreeList(out)
-	if len(wts) != 3 {
-		t.Fatalf("got %d worktrees, want 3: %+v", len(wts), wts)
+	if len(wts) != 5 {
+		t.Fatalf("got %d worktrees, want 5: %+v", len(wts), wts)
 	}
 	if wts[0].Branch != "main" || wts[0].Path != "/home/ben/src/prodenv/repo" {
 		t.Errorf("wt[0] = %+v", wts[0])
@@ -56,6 +66,104 @@ detached
 	if !wts[2].Detached || wts[2].Branch != "" {
 		t.Errorf("wt[2] = %+v, want detached with empty branch", wts[2])
 	}
+	if wts[3].Prunable != "gitdir file points to non-existent location" {
+		t.Errorf("wt[3].Prunable = %q", wts[3].Prunable)
+	}
+	if !wts[4].Locked || wts[4].Prunable != "" {
+		t.Errorf("wt[4] = %+v, want locked and not prunable", wts[4])
+	}
+}
+
+// A bare "prunable" with no reason still has to read as prunable.
+func TestParseWorktreeListPrunableWithoutReason(t *testing.T) {
+	wts := ParseWorktreeList("worktree /tmp/wt\nHEAD 1111111111111111111111111111111111111111\ndetached\nprunable\n")
+	if len(wts) != 1 || wts[0].Prunable == "" {
+		t.Errorf("ParseWorktreeList = %+v, want one prunable worktree", wts)
+	}
+}
+
+func TestGitInProgressOp(t *testing.T) {
+	srcDir := newTempRepos(t)
+	gitDir, err := GitDir(srcDir)
+	if err != nil {
+		t.Fatalf("GitDir: %v", err)
+	}
+	if op, err := GitInProgressOp(srcDir); err != nil || op != "" {
+		t.Fatalf("clean checkout: op = %q, err = %v", op, err)
+	}
+
+	tests := []struct {
+		marker string
+		dir    bool
+		want   string
+	}{
+		{"MERGE_HEAD", false, "merge"},
+		{"CHERRY_PICK_HEAD", false, "cherry-pick"},
+		{"REVERT_HEAD", false, "revert"},
+		{"BISECT_LOG", false, "bisect"},
+		{"rebase-merge", true, "rebase"},
+		{"rebase-apply", true, "rebase"},
+	}
+	for _, tt := range tests {
+		path := filepath.Join(gitDir, tt.marker)
+		if tt.dir {
+			if err := os.Mkdir(path, 0o755); err != nil {
+				t.Fatal(err)
+			}
+		} else if err := os.WriteFile(path, []byte("x\n"), 0o644); err != nil {
+			t.Fatal(err)
+		}
+		op, err := GitInProgressOp(srcDir)
+		if err != nil || op != tt.want {
+			t.Errorf("%s: op = %q, err = %v; want %q", tt.marker, op, err, tt.want)
+		}
+		if err := os.RemoveAll(path); err != nil {
+			t.Fatal(err)
+		}
+	}
+}
+
+// Commits that reached a remote-tracking ref are not unique local work; commits
+// made after the push are.
+func TestGitCommitsNotOnRemotes(t *testing.T) {
+	srcDir := newTempRepos(t)
+	if n, err := GitCommitsNotOnRemotes(srcDir); err != nil || n != 0 {
+		t.Fatalf("freshly cloned main: n = %d, err = %v; want 0", n, err)
+	}
+
+	if _, err := runGit(srcDir, "checkout", "-b", "benvin/x"); err != nil {
+		t.Fatal(err)
+	}
+	commitFile(t, srcDir, "a.txt", "a\n", "local a")
+	commitFile(t, srcDir, "b.txt", "b\n", "local b")
+	if n, err := GitCommitsNotOnRemotes(srcDir); err != nil || n != 2 {
+		t.Fatalf("two unpushed commits: n = %d, err = %v; want 2", n, err)
+	}
+
+	if _, err := runGit(srcDir, "push", "origin", "benvin/x"); err != nil {
+		t.Fatal(err)
+	}
+	if n, err := GitCommitsNotOnRemotes(srcDir); err != nil || n != 0 {
+		t.Fatalf("after push: n = %d, err = %v; want 0", n, err)
+	}
+
+	commitFile(t, srcDir, "c.txt", "c\n", "local c")
+	if n, err := GitCommitsNotOnRemotes(srcDir); err != nil || n != 1 {
+		t.Fatalf("one commit past the push: n = %d, err = %v; want 1", n, err)
+	}
+}
+
+func commitFile(t *testing.T, dir, name, content, msg string) {
+	t.Helper()
+	if err := os.WriteFile(filepath.Join(dir, name), []byte(content), 0o644); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := runGit(dir, "add", "."); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := runGit(dir, "commit", "-m", msg); err != nil {
+		t.Fatal(err)
+	}
 }
 
 // gitSeed sets a repo-local identity so commits work without global config.