@mindfoldhq/trellis 0.6.0-beta.10 → 0.6.0-beta.12

package/dist/templates/markdown/spec/guides/cross-layer-thinking-guide.md.txt

@@ -71,6 +71,35 @@ For each boundary:
 
 **Good**: Each layer only knows its neighbors
 
+### Mistake 4: Every Consumer Parses The Same Payload
+
+**Bad**: A command reads JSONL events and casts fields inline:
+
+```typescript
+const thread = (ev as { thread?: string }).thread;
+const labels = (ev as { labels?: string[] }).labels;
+```
+
+This looks local, but it means every consumer owns a private version of the
+event contract. The next field change will update one command and miss another.
+
+**Good**: Decode once at the event boundary, then export typed projections:
+
+```typescript
+if (!isThreadEvent(ev)) return false;
+return ev.thread === filter.thread;
+```
+
+**Rule**: For append-only logs, JSON streams, RPC payloads, or config files,
+create one owner for:
+
+- event / payload type definitions
+- type guards and normalization from `unknown`
+- metadata projections used by UI commands
+- reducers that replay state from the source of truth
+
+Rendering code may format fields, but it must not redefine the payload contract.
+
 ---
 
 ## Checklist for Cross-Layer Features
@@ -87,6 +116,10 @@ After implementation:
 - [ ] Tested with edge cases (null, empty, invalid)
 - [ ] Verified error handling at each boundary
 - [ ] Checked data survives round-trip
+- [ ] Checked that consumers import shared decoders / projections instead of
+      casting payload fields locally
+- [ ] Checked that derived state points back to the source event identifier
+      (`seq`, `id`, `version`) instead of inventing a second cursor
 
 ---
 
@@ -195,3 +228,32 @@ Create detailed flow docs when:
 - Multiple teams are involved
 - Data format is complex
 - Feature has caused bugs before
+
+---
+
+## Event Log / Projection Boundary
+
+Append-only logs are cross-layer contracts. A single event travels through:
+
+```
+CLI input → event writer → events.jsonl → reader → filter → reducer → display
+```
+
+### Checklist: After Adding A New Event Kind Or Field
+
+- [ ] Add the event kind to the central event taxonomy
+- [ ] Add a typed event variant or type guard at the event layer
+- [ ] Add normalization helpers for array/object fields that come from
+      user input or JSON
+- [ ] Keep `seq` / `id` assignment in the event writer only
+- [ ] Make filters and reducers consume the typed event guard, not local casts
+- [ ] Make display code consume reducer output or typed events, not raw JSON
+- [ ] Add at least one regression that proves history replay and live filtering
+      use the same filter model
+
+**Real-world example**: Thread channels added `kind: "thread"`, `description`,
+`linkedContext`, labels, and `lastSeq`. The first implementation replayed state
+correctly, but several commands still re-parsed event payload fields with local
+casts. The fix was to make `store/events.ts` own `ThreadChannelEvent`,
+`isThreadEvent`, and `metadataFromCreateEvent`, while `store/thread-state.ts`
+became the only replay reducer.

package/dist/templates/markdown/spec/guides/index.md.txt

@@ -34,6 +34,8 @@ These guides help you **ask the right questions before coding**.
 - [ ] Data format changes between layers
 - [ ] Multiple consumers need the same data
 - [ ] You're not sure where to put some logic
+- [ ] You are adding an event kind, JSONL record, RPC payload, or config field
+- [ ] UI / command code starts casting raw payload fields directly
 
 → Read [Cross-Layer Thinking Guide](./cross-layer-thinking-guide.md)
 
@@ -44,9 +46,25 @@ These guides help you **ask the right questions before coding**.
 - [ ] You're adding a new field to multiple places
 - [ ] **You're modifying any constant or config**
 - [ ] **You're creating a new utility/helper function** ← Search first!
+- [ ] Two files read the same untyped payload field with local casts
+- [ ] Multiple branches update the same derived state from `kind` / `action`
 
 → Read [Code Reuse Thinking Guide](./code-reuse-thinking-guide.md)
 
+### When Verifying AI Cross-Review Results
+
+- [ ] Reviewer claims "user input can be malicious" → Check the actual data source (internal manifest? user config? external API?)
+- [ ] Reviewer flags "missing validation" → Is the data from a trusted internal source?
+- [ ] Reviewer says "behavior change" → Read the code comments — is it intentional design?
+- [ ] Reviewer identifies a "bug" in test → Mentally delete the feature being tested — does the test still pass? If yes → tautological test
+
+**Common AI reviewer false-positive patterns**:
+1. **Trust boundary confusion**: Treating internal data (bundled JSON manifests) as untrusted external input
+2. **Ignoring design comments**: Flagging intentional behavior documented in code comments as bugs
+3. **Variable misreading**: Not tracing a variable to its actual definition (e.g., Map keyed by path vs name)
+
+**Verification rule**: Every CRITICAL/WARNING finding must be verified against the actual code before prioritizing. Budget ~35% false-positive rate for AI reviews.
+
 ---
 
 ## Pre-Modification Rule (CRITICAL)

package/dist/templates/shared-hooks/inject-workflow-state.py

@@ -33,6 +33,28 @@ import os
 import re
 import sys
 from pathlib import Path
+
+# Force UTF-8 on stdin/stdout/stderr on Windows. Default codepage there is
+# cp936 / cp1252 / etc. — non-ASCII content (Chinese task names, prd snippets)
+# both in stdin (hook payload from host CLI) and stdout (our emitted blocks)
+# raises UnicodeDecodeError / UnicodeEncodeError. Equivalent to `python -X utf8`
+# but applied per-stream so we don't depend on host CLI's command wiring.
+if sys.platform.startswith("win"):
+    import io as _io
+    for _stream_name in ("stdin", "stdout", "stderr"):
+        _stream = getattr(sys, _stream_name, None)
+        if _stream is None:
+            continue
+        if hasattr(_stream, "reconfigure"):
+            try:
+                _stream.reconfigure(encoding="utf-8", errors="replace")  # type: ignore[union-attr]
+            except Exception:
+                pass
+        elif hasattr(_stream, "detach"):
+            try:
+                setattr(sys, _stream_name, _io.TextIOWrapper(_stream.detach(), encoding="utf-8", errors="replace"))
+            except Exception:
+                pass
 from typing import Optional
 
 

package/dist/templates/shared-hooks/session-start.py

@@ -72,14 +72,27 @@ First visible reply: say once in Chinese that Trellis SessionStart context is lo
 This notice is one-shot: do not repeat it after the first assistant reply in the same session.
 </first-reply-notice>"""
 
-# IMPORTANT: Force stdout to use UTF-8 on Windows
-# This fixes UnicodeEncodeError when outputting non-ASCII characters
+# Force UTF-8 on stdin/stdout/stderr on Windows. Default codepage there is
+# cp936 / cp1252 / etc. — non-ASCII content (Chinese task names, prd snippets)
+# both in stdin (hook payload from host CLI) and stdout (our emitted blocks)
+# raises UnicodeDecodeError / UnicodeEncodeError. Equivalent to `python -X utf8`
+# but applied per-stream so we don't depend on host CLI's command wiring.
 if sys.platform.startswith("win"):
     import io as _io
-    if hasattr(sys.stdout, "reconfigure"):
-        sys.stdout.reconfigure(encoding="utf-8", errors="replace")  # type: ignore[union-attr]
-    elif hasattr(sys.stdout, "detach"):
-        sys.stdout = _io.TextIOWrapper(sys.stdout.detach(), encoding="utf-8", errors="replace")  # type: ignore[union-attr]
+    for _stream_name in ("stdin", "stdout", "stderr"):
+        _stream = getattr(sys, _stream_name, None)
+        if _stream is None:
+            continue
+        if hasattr(_stream, "reconfigure"):
+            try:
+                _stream.reconfigure(encoding="utf-8", errors="replace")  # type: ignore[union-attr]
+            except Exception:
+                pass
+        elif hasattr(_stream, "detach"):
+            try:
+                setattr(sys, _stream_name, _io.TextIOWrapper(_stream.detach(), encoding="utf-8", errors="replace"))
+            except Exception:
+                pass
 
 
 

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

@@ -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") {

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