@mindfoldhq/trellis 0.5.13 → 0.5.15

package/dist/templates/trellis/scripts/common/safe_commit.py

@@ -111,31 +111,61 @@ def safe_trellis_paths_to_add(repo_root: Path) -> list[str]:
     return paths
 
 
-def safe_archive_paths_to_add(repo_root: Path) -> list[str]:
+def safe_archive_paths_to_add(
+    repo_root: Path,
+    task_name: str | None = None,
+    modified_children: list[str] | None = None,
+) -> list[str]:
     """Return paths to stage after `task.py archive`.
 
-    Limited to the archive subtree (where the freshly-moved task lives) plus
-    the source task directory's parent area to capture the deletion in the
-    same commit. We pass the whole `.trellis/tasks/` path so deletions of the
-    pre-move path are tracked, but only as a SPECIFIC subpath — not the whole
-    `.trellis/` tree.
+    Scoped to ONLY the paths the archive operation actually touched:
+
+      - the archive subtree (where the freshly-moved task lives)
+      - the source task directory (for source-side deletes; caller pairs
+        this with `git rm --cached` since `git add` won't stage deletes
+        for a path that no longer exists in the working tree)
+      - any child task directories whose `task.json` was edited to drop
+        the archived parent (parent-children relationship update)
+
+    This narrow scope avoids "scope creep" — dirty changes in OTHER
+    active task dirs (parallel-window edits) are NOT bundled into the
+    archive commit. Callers handle each kind of change in its own
+    commit boundary.
+
+    Backwards-compat: with no arguments, the function walks the whole
+    `.trellis/tasks/` subtree the old way (active tasks + archive). New
+    callers should always pass `task_name`.
     """
     paths: list[str] = []
     tasks_dir = repo_root / DIR_WORKFLOW / DIR_TASKS
-    if tasks_dir.is_dir():
-        # The archive copy.
-        archive_dir = tasks_dir / DIR_ARCHIVE
+    if not tasks_dir.is_dir():
+        return paths
+
+    archive_dir = tasks_dir / DIR_ARCHIVE
+
+    if task_name is not None:
+        # Narrow scope — only paths that still exist on disk (so
+        # `git add` doesn't choke on the moved-away source). The caller
+        # handles the source-side deletes via `git rm --cached`
+        # explicitly.
         if archive_dir.is_dir():
-            paths.append(f"{DIR_WORKFLOW}/{DIR_TASKS}/{DIR_ARCHIVE}")
-        # Active tasks (some may have been re-touched, e.g. parent's
-        # children list). This captures the source-path deletion too because
-        # `git add` on a directory records removals.
-        for child in sorted(tasks_dir.iterdir()):
-            if not child.is_dir():
-                continue
-            if child.name == DIR_ARCHIVE:
-                continue
-            paths.append(f"{DIR_WORKFLOW}/{DIR_TASKS}/{child.name}")
+            paths.append(
+                f"{DIR_WORKFLOW}/{DIR_TASKS}/{DIR_ARCHIVE}"
+            )
+        for child_name in modified_children or []:
+            paths.append(f"{DIR_WORKFLOW}/{DIR_TASKS}/{child_name}")
+        return paths
+
+    # Legacy wide scope (no task_name): preserve old behavior so callers
+    # that have not been updated keep working.
+    if archive_dir.is_dir():
+        paths.append(f"{DIR_WORKFLOW}/{DIR_TASKS}/{DIR_ARCHIVE}")
+    for child in sorted(tasks_dir.iterdir()):
+        if not child.is_dir():
+            continue
+        if child.name == DIR_ARCHIVE:
+            continue
+        paths.append(f"{DIR_WORKFLOW}/{DIR_TASKS}/{child.name}")
     return paths
 
 

package/dist/templates/trellis/scripts/common/task_store.py

@@ -337,6 +337,9 @@ def cmd_archive(args: argparse.Namespace) -> int:
 
     # Update status before archiving
     today = datetime.now().strftime("%Y-%m-%d")
+    # Names of child task dirs whose task.json gets modified below; passed
+    # into safe_archive_paths_to_add so they're staged in this commit.
+    modified_children: list[str] = []
     if task_json_path.is_file():
         data = read_json(task_json_path)
         if data:
@@ -361,6 +364,7 @@ def cmd_archive(args: argparse.Namespace) -> int:
                             if child_data:
                                 child_data["parent"] = None
                                 write_json(child_json, child_data)
+                                modified_children.append(child_dir_path.name)
 
     # Clear any session that still points at this task before the path moves.
     from .active_task import clear_task_from_sessions
@@ -375,7 +379,7 @@ def cmd_archive(args: argparse.Namespace) -> int:
 
         # Auto-commit unless --no-commit
         if not getattr(args, "no_commit", False):
-            _auto_commit_archive(dir_name, repo_root)
+            _auto_commit_archive(dir_name, repo_root, modified_children)
 
         # Return the archive path
         print(f"{DIR_WORKFLOW}/{DIR_TASKS}/{DIR_ARCHIVE}/{year_month}/{dir_name}")
@@ -388,18 +392,26 @@ def cmd_archive(args: argparse.Namespace) -> int:
     return 1
 
 
-def _auto_commit_archive(task_name: str, repo_root: Path) -> None:
+def _auto_commit_archive(
+    task_name: str,
+    repo_root: Path,
+    modified_children: list[str] | None = None,
+) -> None:
     """Stage Trellis-owned task paths and commit after archive.
 
-    Only stages specific subpaths (the archive subtree and active task dirs),
-    never the whole ``.trellis/`` tree. If ``.gitignore`` blocks the paths,
-    we warn + skip — we do NOT retry with ``git add -f``. The warning
-    explicitly forbids ``git add -f .trellis/`` (which would fan out to
-    caches/backups) and points users at ``session_auto_commit: false``.
+    Scoped narrowly to the archived task's source + destination paths
+    plus any child task dirs whose ``task.json`` was edited (parent →
+    children relationship update). Dirty changes in OTHER active task
+    dirs are NOT bundled into the archive commit.
 
-    Honors ``session_auto_commit`` in ``.trellis/config.yaml``: when set to
-    ``false``, this function returns immediately without touching git
-    (the archive directory move on disk is unaffected).
+    If ``.gitignore`` blocks the paths, we warn + skip — we do NOT
+    retry with ``git add -f``. The warning explicitly forbids
+    ``git add -f .trellis/`` (which would fan out to caches/backups)
+    and points users at ``session_auto_commit: false``.
+
+    Honors ``session_auto_commit`` in ``.trellis/config.yaml``: when
+    set to ``false``, this function returns immediately without
+    touching git (the archive directory move on disk is unaffected).
     """
     if not get_session_auto_commit(repo_root):
         print(
@@ -408,7 +420,9 @@ def _auto_commit_archive(task_name: str, repo_root: Path) -> None:
         )
         return
 
-    paths = safe_archive_paths_to_add(repo_root)
+    paths = safe_archive_paths_to_add(
+        repo_root, task_name=task_name, modified_children=modified_children
+    )
     if not paths:
         print("[OK] No task changes to commit.", file=sys.stderr)
         return
@@ -424,8 +438,24 @@ def _auto_commit_archive(task_name: str, repo_root: Path) -> None:
             )
         return
 
+    # Belt-and-suspenders for the phantom-delete bug: `safe_git_add` uses
+    # `git add` (no -A) which only stages additions/modifications. The
+    # source task directory was moved away by `shutil.move`, so its files
+    # need an explicit `git rm --cached` to stage the deletions in this
+    # same commit — otherwise they sit as uncommitted "phantom deletes"
+    # against HEAD until something later picks them up.
+    #
+    # `--ignore-unmatch` makes this a no-op when the task was never tracked
+    # (e.g. archiving a task that lived only in working tree).
+    source_rel = f"{DIR_WORKFLOW}/{DIR_TASKS}/{task_name}"
+    run_git(
+        ["rm", "-r", "--cached", "--ignore-unmatch", "--", source_rel],
+        cwd=repo_root,
+    )
+
     rc, _, _ = run_git(
-        ["diff", "--cached", "--quiet", "--", *paths], cwd=repo_root
+        ["diff", "--cached", "--quiet", "--", *paths, source_rel],
+        cwd=repo_root,
     )
     if rc == 0:
         print("[OK] No task changes to commit.", file=sys.stderr)

package/dist/utils/cwd-guard.d.ts

@@ -0,0 +1,38 @@
+/**
+ * Homedir guard for destructive commands (init, uninstall).
+ *
+ * Running `trellis init` / `trellis uninstall` in `$HOME` is catastrophic:
+ * platforms like Claude Code, Codex, OpenCode all store global runtime data
+ * (`.claude/projects/<sanitized-cwd>/*.jsonl` chat history, `.codex/sessions/`,
+ * `.opencode/` caches, etc.) directly in the user's home directory. If
+ * trellis manages the same `.{platform}/` config dirs and the hash manifest
+ * picks up runtime data, uninstall would later unlink it.
+ *
+ * Subdirectories of home (`~/Documents/projects/foo/`) are NOT blocked — only
+ * exact-home match.
+ *
+ * Bypass: `TRELLIS_ALLOW_HOMEDIR=1`.
+ */
+/**
+ * Returns true if `process.cwd()` is exactly the user's home directory.
+ *
+ * Uses `realpathSync.native()` on both sides so symlinks, `..` segments, and
+ * case differences (Windows) don't confuse the comparison. On Windows the
+ * comparison is also case-insensitive — `C:\Users\Alice` matches
+ * `c:\users\alice`.
+ *
+ * Permissive on lookup failure: if realpath fails for any reason (broken
+ * symlink, EACCES, etc.) we return false so a safety check doesn't crash
+ * the command.
+ */
+export declare function isCwdHomedir(): boolean;
+/**
+ * Error message printed by both `trellis init` and `trellis uninstall` when
+ * the homedir guard trips.
+ */
+export declare function homedirGuardMessage(commandName: "init" | "uninstall"): string;
+/**
+ * Returns true when the bypass env var is set.
+ */
+export declare function homedirBypassEnabled(): boolean;
+//# sourceMappingURL=cwd-guard.d.ts.map

package/dist/utils/cwd-guard.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cwd-guard.d.ts","sourceRoot":"","sources":["../../src/utils/cwd-guard.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAKH;;;;;;;;;;;GAWG;AACH,wBAAgB,YAAY,IAAI,OAAO,CAYtC;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,WAAW,GAAG,MAAM,CAS7E;AAED;;GAEG;AACH,wBAAgB,oBAAoB,IAAI,OAAO,CAE9C"}

package/dist/utils/cwd-guard.js

@@ -0,0 +1,62 @@
+/**
+ * Homedir guard for destructive commands (init, uninstall).
+ *
+ * Running `trellis init` / `trellis uninstall` in `$HOME` is catastrophic:
+ * platforms like Claude Code, Codex, OpenCode all store global runtime data
+ * (`.claude/projects/<sanitized-cwd>/*.jsonl` chat history, `.codex/sessions/`,
+ * `.opencode/` caches, etc.) directly in the user's home directory. If
+ * trellis manages the same `.{platform}/` config dirs and the hash manifest
+ * picks up runtime data, uninstall would later unlink it.
+ *
+ * Subdirectories of home (`~/Documents/projects/foo/`) are NOT blocked — only
+ * exact-home match.
+ *
+ * Bypass: `TRELLIS_ALLOW_HOMEDIR=1`.
+ */
+import { realpathSync } from "node:fs";
+import * as os from "node:os";
+/**
+ * Returns true if `process.cwd()` is exactly the user's home directory.
+ *
+ * Uses `realpathSync.native()` on both sides so symlinks, `..` segments, and
+ * case differences (Windows) don't confuse the comparison. On Windows the
+ * comparison is also case-insensitive — `C:\Users\Alice` matches
+ * `c:\users\alice`.
+ *
+ * Permissive on lookup failure: if realpath fails for any reason (broken
+ * symlink, EACCES, etc.) we return false so a safety check doesn't crash
+ * the command.
+ */
+export function isCwdHomedir() {
+    try {
+        let cwd = realpathSync.native(process.cwd());
+        let home = realpathSync.native(os.homedir());
+        if (process.platform === "win32") {
+            cwd = cwd.toLowerCase();
+            home = home.toLowerCase();
+        }
+        return cwd === home;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Error message printed by both `trellis init` and `trellis uninstall` when
+ * the homedir guard trips.
+ */
+export function homedirGuardMessage(commandName) {
+    return (`✗ Refusing to run \`trellis ${commandName}\` in your home directory.\n\n` +
+        `Trellis manages platform config dirs like .claude/, .codex/, .opencode/, which\n` +
+        `in your home directory also contain runtime data from those CLIs (chat history,\n` +
+        `session JSONLs, caches). Running here can wipe that data.\n\n` +
+        `Run trellis from your project directory instead. If you really want to run in\n` +
+        `$HOME, set TRELLIS_ALLOW_HOMEDIR=1.`);
+}
+/**
+ * Returns true when the bypass env var is set.
+ */
+export function homedirBypassEnabled() {
+    return process.env.TRELLIS_ALLOW_HOMEDIR === "1";
+}
+//# sourceMappingURL=cwd-guard.js.map

package/dist/utils/cwd-guard.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cwd-guard.js","sourceRoot":"","sources":["../../src/utils/cwd-guard.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAE9B;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,YAAY;IAC1B,IAAI,CAAC;QACH,IAAI,GAAG,GAAG,YAAY,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC;QAC7C,IAAI,IAAI,GAAG,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC;QAC7C,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE,CAAC;YACjC,GAAG,GAAG,GAAG,CAAC,WAAW,EAAE,CAAC;YACxB,IAAI,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QAC5B,CAAC;QACD,OAAO,GAAG,KAAK,IAAI,CAAC;IACtB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CAAC,WAAiC;IACnE,OAAO,CACL,+BAA+B,WAAW,gCAAgC;QAC1E,kFAAkF;QAClF,mFAAmF;QACnF,+DAA+D;QAC/D,iFAAiF;QACjF,qCAAqC,CACtC,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,oBAAoB;IAClC,OAAO,OAAO,CAAC,GAAG,CAAC,qBAAqB,KAAK,GAAG,CAAC;AACnD,CAAC"}

package/dist/utils/file-writer.d.ts

@@ -4,6 +4,19 @@ export interface WriteOptions {
 }
 export declare function setWriteMode(mode: WriteMode): void;
 export declare function getWriteMode(): WriteMode;
+/**
+ * Begin recording every write into the returned Set. Calls accumulate into the
+ * same set until `stopRecordingWrites` runs. POSIX relative paths (relative to
+ * `cwd`) are stored, matching `.template-hashes.json` keys.
+ *
+ * Nested recording sessions are NOT supported — the caller must ensure
+ * `stopRecordingWrites` runs before the next `startRecordingWrites`. Failure
+ * is silent (the second `start` replaces the first set), so callers should
+ * always pair start/stop in try/finally.
+ */
+export declare function startRecordingWrites(cwd: string): Set<string>;
+/** End recording. Subsequent writes are not captured until `start` is called again. */
+export declare function stopRecordingWrites(): void;
 /**
  * Write file with conflict handling
  * - If file doesn't exist: write directly

package/dist/utils/file-writer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"file-writer.d.ts","sourceRoot":"","sources":["../../src/utils/file-writer.ts"],"names":[],"mappings":"AAKA,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,OAAO,GAAG,MAAM,GAAG,QAAQ,CAAC;AAE5D,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,SAAS,CAAC;CACjB;AASD,wBAAgB,YAAY,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI,CAElD;AAED,wBAAgB,YAAY,IAAI,SAAS,CAExC;AA6BD;;;;;;;;GAQG;AACH,wBAAsB,SAAS,CAC7B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,MAAM,EACf,OAAO,CAAC,EAAE;IAAE,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACjC,OAAO,CAAC,OAAO,CAAC,CA8GlB;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE/C"}
+{"version":3,"file":"file-writer.d.ts","sourceRoot":"","sources":["../../src/utils/file-writer.ts"],"names":[],"mappings":"AAOA,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,OAAO,GAAG,MAAM,GAAG,QAAQ,CAAC;AAE5D,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,SAAS,CAAC;CACjB;AASD,wBAAgB,YAAY,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI,CAElD;AAED,wBAAgB,YAAY,IAAI,SAAS,CAExC;AAkBD;;;;;;;;;GASG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAK7D;AAED,uFAAuF;AACvF,wBAAgB,mBAAmB,IAAI,IAAI,CAG1C;AAsCD;;;;;;;;GAQG;AACH,wBAAsB,SAAS,CAC7B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,MAAM,EACf,OAAO,CAAC,EAAE;IAAE,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACjC,OAAO,CAAC,OAAO,CAAC,CA0HlB;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE/C"}

package/dist/utils/file-writer.js

@@ -2,6 +2,7 @@ import fs from "node:fs";
 import path from "node:path";
 import chalk from "chalk";
 import inquirer from "inquirer";
+import { toPosix } from "./posix.js";
 // Global write mode (set from CLI options)
 let globalWriteMode = "ask";
 export function setWriteMode(mode) {
@@ -10,6 +11,51 @@ export function setWriteMode(mode) {
 export function getWriteMode() {
     return globalWriteMode;
 }
+// ---------------------------------------------------------------------------
+// Write recording
+//
+// `trellis init` uses recording to capture exactly which files were actually
+// written this run (vs skipped because they already existed). The captured
+// set is what `.template-hashes.json` should contain — NOT a blind directory
+// walk of `.codex/` / `.claude/` / etc, which would include user-owned files
+// that pre-dated init. See `pruneOrphanManifestKeys` for the self-heal side
+// of the same contract.
+// ---------------------------------------------------------------------------
+/** When recording is active, every actual `writeFile` disk write appends here. */
+let writeRecorder = null;
+/** Project root used to convert absolute write paths to POSIX-relative keys. */
+let writeRecorderRoot = null;
+/**
+ * Begin recording every write into the returned Set. Calls accumulate into the
+ * same set until `stopRecordingWrites` runs. POSIX relative paths (relative to
+ * `cwd`) are stored, matching `.template-hashes.json` keys.
+ *
+ * Nested recording sessions are NOT supported — the caller must ensure
+ * `stopRecordingWrites` runs before the next `startRecordingWrites`. Failure
+ * is silent (the second `start` replaces the first set), so callers should
+ * always pair start/stop in try/finally.
+ */
+export function startRecordingWrites(cwd) {
+    const sink = new Set();
+    writeRecorder = sink;
+    writeRecorderRoot = cwd;
+    return sink;
+}
+/** End recording. Subsequent writes are not captured until `start` is called again. */
+export function stopRecordingWrites() {
+    writeRecorder = null;
+    writeRecorderRoot = null;
+}
+/** Record a successful write. Called internally by `writeFile`. */
+function recordWrite(absPath) {
+    if (!writeRecorder || !writeRecorderRoot)
+        return;
+    const rel = path.relative(writeRecorderRoot, absPath);
+    // Defensive: skip writes outside cwd (no meaningful manifest key).
+    if (rel.startsWith("..") || path.isAbsolute(rel))
+        return;
+    writeRecorder.add(toPosix(rel));
+}
 /**
  * Get relative path from cwd for display
  */
@@ -49,12 +95,15 @@ export async function writeFile(filePath, content, options) {
         if (options?.executable) {
             fs.chmodSync(filePath, "755");
         }
+        recordWrite(filePath);
         return true;
     }
     // File exists, check if content is identical
     const existingContent = fs.readFileSync(filePath, "utf-8");
     if (existingContent === content) {
-        // Content identical, skip silently (no output)
+        // Content identical, but no disk write happened. Do not record it for
+        // init-time manifests: pre-existing user files can legitimately be
+        // byte-identical to a Trellis template and still not be Trellis-owned.
         return false;
     }
     // File exists with different content, handle based on mode.
@@ -70,15 +119,22 @@ export async function writeFile(filePath, content, options) {
             fs.chmodSync(filePath, "755");
         }
         console.log(chalk.yellow(`  ↻ Overwritten: ${displayPath}`));
+        recordWrite(filePath);
         return true;
     }
     if (mode === "skip") {
         console.log(chalk.gray(`  ○ Skipped: ${displayPath} (already exists)`));
+        // Skipped: trellis did NOT write this file — caller should not track it
+        // in the manifest. This is the AGENTS.md skip-existing case.
         return false;
     }
     if (mode === "append") {
         appendToFile(filePath, content, options);
         console.log(chalk.blue(`  + Appended: ${displayPath}`));
+        // Append: trellis added trellis content to a user-owned file. Tracking
+        // is risky here (uninstall would unlink the whole file), so we do NOT
+        // record appended files. Users on `--append` get a fresh manifest miss
+        // on next update; that's the safer default.
         return true;
     }
     // mode === 'ask': Interactive prompt
@@ -107,6 +163,7 @@ export async function writeFile(filePath, content, options) {
             fs.chmodSync(filePath, "755");
         }
         console.log(chalk.yellow(`  ↻ Overwritten: ${displayPath}`));
+        recordWrite(filePath);
         return true;
     }
     if (action === "append") {
@@ -126,6 +183,7 @@ export async function writeFile(filePath, content, options) {
             fs.chmodSync(filePath, "755");
         }
         console.log(chalk.yellow(`  ↻ Overwritten: ${displayPath}`));
+        recordWrite(filePath);
         return true;
     }
     if (action === "append-all") {

package/dist/utils/file-writer.js.map

@@ -1 +1 @@
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package/dist/utils/manifest-prune.d.ts

@@ -0,0 +1,61 @@
+/**
+ * Self-heal poisoned `.template-hashes.json` manifests.
+ *
+ * Versions before this fix walked `.codex/`, `.claude/`, etc. with a blind
+ * recursive scan when computing the manifest, so they hashed user-owned
+ * runtime data (`.codex/sessions/*`, `.claude/projects/*.jsonl`, pre-existing
+ * `AGENTS.md`, user-added `.codex/skills/<custom>/`, …). On uninstall, every
+ * manifest entry is unlinked, which silently deletes user data.
+ *
+ * `pruneOrphanManifestKeys` removes any manifest entry that no current
+ * platform configurator owns. The two entry points that consume it are
+ * `trellis update` (before migration classification) and `trellis uninstall`
+ * (before plan building). Together they ensure existing poisoned manifests
+ * self-correct on the next routine command.
+ *
+ * Rules:
+ *   - `.trellis/*` entries are ALWAYS kept. `trellis uninstall` removes
+ *     `.trellis/` wholesale via `fs.rmSync(..., { recursive: true })`, so
+ *     manifest accuracy there doesn't affect uninstall data-loss. `update`
+ *     also relies on these entries to detect user-modified workflow files.
+ *   - Root-level `AGENTS.md` is kept only when it still looks Trellis-managed
+ *     (contains the managed block markers) or is missing on disk. This
+ *     self-heals old poisoned manifests for user-owned AGENTS.md files that
+ *     predated init and were skipped.
+ *   - Paths referenced by `from`/`to` of any migration manifest entry
+ *     (rename, rename-dir, delete, safe-file-delete) are preserved. Pruning
+ *     them would prevent legitimate pending migrations from finding their
+ *     source/target.
+ *   - Everything else: if the path is not in the union of
+ *     `collectPlatformTemplates()` for currently-configured platforms, it is
+ *     pruned. This matches "files trellis actually wrote during init/update".
+ */
+import type { AITool } from "../types/ai-tools.js";
+import type { TemplateHashes } from "../types/migration.js";
+export interface PruneResult {
+    /** Manifest keys removed (POSIX-style relative paths). */
+    pruned: string[];
+    /** The post-prune manifest (saved to disk only when `pruned.length > 0`). */
+    hashes: TemplateHashes;
+}
+export interface PruneOptions {
+    /**
+     * Save the pruned manifest to `.template-hashes.json`. Defaults to true.
+     * Callers can pass `false` to compute the prune without mutating disk
+     * (dry-run, change-analysis passes).
+     */
+    persist?: boolean;
+}
+/**
+ * Walk the manifest and split it into kept vs pruned entries.
+ *
+ * @param cwd  Project root — used to save the rewritten manifest.
+ * @param configuredPlatforms Output of `getConfiguredPlatforms(cwd)` — caller
+ *   resolves this so we don't have to re-walk the filesystem.
+ * @param hashes Already-loaded manifest contents. Passing it in (vs reading
+ *   from disk) lets the caller chain `loadHashes` → prune → use the result.
+ * @param options.persist When true (default), saves the pruned manifest to
+ *   disk. Pass `false` for dry-run flows.
+ */
+export declare function pruneOrphanManifestKeys(cwd: string, configuredPlatforms: readonly AITool[], hashes: TemplateHashes, options?: PruneOptions): PruneResult;
+//# sourceMappingURL=manifest-prune.d.ts.map

package/dist/utils/manifest-prune.d.ts.map

@@ -0,0 +1 @@
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