@mindfoldhq/trellis 0.6.0-beta.10 → 0.6.0-beta.11

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

@@ -369,6 +369,9 @@ 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:
@@ -393,6 +396,7 @@ 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
@@ -407,7 +411,7 @@ 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}")
@@ -420,18 +424,26 @@ 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(
@@ -440,7 +452,9 @@ 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
@@ -456,8 +470,24 @@ 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 @@
+{"version":3,"file":"manifest-prune.d.ts","sourceRoot":"","sources":["../../src/utils/manifest-prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAUH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAK5D,MAAM,WAAW,WAAW;IAC1B,0DAA0D;IAC1D,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,6EAA6E;IAC7E,MAAM,EAAE,cAAc,CAAC;CACxB;AAoDD,MAAM,WAAW,YAAY;IAC3B;;;;OAIG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,uBAAuB,CACrC,GAAG,EAAE,MAAM,EACX,mBAAmB,EAAE,SAAS,MAAM,EAAE,EACtC,MAAM,EAAE,cAAc,EACtB,OAAO,GAAE,YAAiB,GACzB,WAAW,CAmCb"}

package/dist/utils/manifest-prune.js

@@ -0,0 +1,136 @@
+/**
+ * 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 fs from "node:fs";
+import path from "node:path";
+import { collectPlatformTemplates } from "../configurators/index.js";
+import { FILE_NAMES } from "../constants/paths.js";
+import { getAllMigrations } from "../migrations/index.js";
+import { saveHashes } from "./template-hash.js";
+import { toPosix } from "./posix.js";
+const TRELLIS_BLOCK_START = "<!-- TRELLIS:START -->";
+const TRELLIS_BLOCK_END = "<!-- TRELLIS:END -->";
+/**
+ * Compute the union of "what trellis writes" across:
+ *   - every configured platform's collectTemplates() output
+ *   - root-level AGENTS.md when it still carries Trellis managed-block markers
+ *   - every migration manifest's from/to path (preserve so legitimate
+ *     pending migrations can find their source/target)
+ */
+function buildKnownKeys(configuredPlatforms) {
+    const known = new Set();
+    for (const id of configuredPlatforms) {
+        const templates = collectPlatformTemplates(id);
+        if (!templates)
+            continue;
+        for (const key of templates.keys()) {
+            known.add(toPosix(key));
+        }
+    }
+    // Preserve any path referenced by a migration: legitimate pending
+    // rename/delete operations need to resolve their `from` (and the target's
+    // hash record for `to`) even if the current registry doesn't list it.
+    for (const migration of getAllMigrations()) {
+        if (migration.from)
+            known.add(toPosix(migration.from));
+        if (migration.to)
+            known.add(toPosix(migration.to));
+    }
+    return known;
+}
+/**
+ * Root-level AGENTS.md needs special handling because it has no platform
+ * registry owner. New fixed inits record it only when written, but old
+ * manifests may contain a user-owned AGENTS.md that init skipped. The
+ * managed block markers are the least destructive ownership signal: no
+ * markers means preserve the user's file by pruning the stale manifest key.
+ */
+function shouldKeepAgentsMd(cwd) {
+    const fullPath = path.join(cwd, FILE_NAMES.AGENTS);
+    if (!fs.existsSync(fullPath)) {
+        return true;
+    }
+    try {
+        const content = fs.readFileSync(fullPath, "utf-8");
+        return (content.includes(TRELLIS_BLOCK_START) &&
+            content.includes(TRELLIS_BLOCK_END));
+    }
+    catch {
+        return true;
+    }
+}
+/**
+ * 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 function pruneOrphanManifestKeys(cwd, configuredPlatforms, hashes, options = {}) {
+    const persist = options.persist ?? true;
+    const known = buildKnownKeys(configuredPlatforms);
+    const pruned = [];
+    const kept = {};
+    for (const [rawKey, value] of Object.entries(hashes)) {
+        const key = toPosix(rawKey);
+        // Always preserve .trellis/ entries — they're for the workflow tree
+        // which uninstall removes wholesale and which update needs for
+        // modified-file detection.
+        if (key.startsWith(".trellis/") || key === ".trellis") {
+            kept[key] = value;
+            continue;
+        }
+        if (key === FILE_NAMES.AGENTS) {
+            if (shouldKeepAgentsMd(cwd)) {
+                kept[key] = value;
+            }
+            else {
+                pruned.push(key);
+            }
+            continue;
+        }
+        if (known.has(key)) {
+            kept[key] = value;
+            continue;
+        }
+        pruned.push(key);
+    }
+    if (persist && pruned.length > 0) {
+        saveHashes(cwd, kept);
+    }
+    return { pruned, hashes: kept };
+}
+//# sourceMappingURL=manifest-prune.js.map

package/dist/utils/manifest-prune.js.map

@@ -0,0 +1 @@
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package/dist/utils/template-hash.d.ts

@@ -83,15 +83,41 @@ export declare function matchesOriginalTemplate(cwd: string, relativePath: strin
  * @returns Map of path to modification status
  */
 export declare function getModificationStatus(cwd: string, relativePaths: string[], hashes: TemplateHashes): Map<string, boolean>;
+/** Options accepted by {@link initializeHashes}. */
+export interface InitializeHashesOptions {
+    /**
+     * POSIX-style relative paths trellis actually wrote during the init run
+     * (captured via `startRecordingWrites` in `file-writer.ts`). Only these
+     * paths are hashed for the platform/root-level coverage; anything else
+     * under `.codex/` / `.claude/` / etc. is left alone, even if it exists
+     * on disk. Setting this to `undefined` or an empty set means "no
+     * platform/root coverage this run" — historical hashes from earlier
+     * runs are preserved via `merge`.
+     */
+    trackedPaths?: ReadonlySet<string>;
+    /**
+     * When true, merge `trackedPaths`-derived hashes into the EXISTING manifest
+     * instead of replacing it. Used by `handleReinit` "add platform" flow so
+     * previously-tracked platforms aren't wiped from the manifest when only
+     * a new platform's writes are recorded. Defaults to false (replace).
+     */
+    merge?: boolean;
+}
 /**
  * Initialize template hashes after init
  *
- * Scans all template directories and computes hashes for files.
- * This should be called at the end of `trellis init` to enable
- * modification detection on subsequent updates.
+ * The platform/root section of the manifest comes from `trackedPaths` —
+ * the set of POSIX paths that `writeFile` actually wrote (or owned with
+ * byte-identical content) during this init run. Avoids the historical bug
+ * where a blind directory walk of `.codex/` / `.claude/` swept up
+ * user-owned runtime data (chat history, session JSONLs).
  *
- * @param cwd - Working directory
- * @returns Number of files hashed
+ * `.trellis/` is still walked recursively (with `EXCLUDE_FROM_HASH`) because
+ * uninstall removes `.trellis/` wholesale via `rm -rf` regardless of manifest
+ * content — accuracy there doesn't affect data-loss, only `trellis update`
+ * 3-way-merge fidelity (preserved by the existing walk).
+ *
+ * @returns Number of files hashed in the final manifest.
  */
-export declare function initializeHashes(cwd: string): number;
+export declare function initializeHashes(cwd: string, options?: InitializeHashesOptions): number;
 //# sourceMappingURL=template-hash.d.ts.map

package/dist/utils/template-hash.d.ts.map

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