@mindfoldhq/trellis 0.5.14 → 0.5.16

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

@@ -73,14 +73,27 @@ Trellis SessionStart 已注入：workflow、当前任务状态、开发者身份
 Then continue directly with the user's request. 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
 
 
 
@@ -765,11 +778,15 @@ When the user sends the first message, follow <task-status> and the workflow gui
 If a task is READY, execute its Next required action without asking whether to continue.
 </ready>""")
 
+    context_text = output.getvalue()
     result = {
+        # Claude Code / Qoder / CodeBuddy / Droid / Gemini / Copilot format
         "hookSpecificOutput": {
             "hookEventName": "SessionStart",
-            "additionalContext": output.getvalue(),
-        }
+            "additionalContext": context_text,
+        },
+        # Cursor sessionStart format (top-level snake_case per Cursor docs)
+        "additional_context": context_text,
     }
 
     # Output JSON - stdout is already configured for UTF-8

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 @@
-{"version":3,"file":"file-writer.js","sourceRoot":"","sources":["../../src/utils/file-writer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,QAAQ,MAAM,UAAU,CAAC;AAYhC,2CAA2C;AAC3C,IAAI,eAAe,GAAc,KAAK,CAAC;AAEvC,MAAM,UAAU,YAAY,CAAC,IAAe;IAC1C,eAAe,GAAG,IAAI,CAAC;AACzB,CAAC;AAED,MAAM,UAAU,YAAY;IAC1B,OAAO,eAAe,CAAC;AACzB,CAAC;AAED;;GAEG;AACH,SAAS,eAAe,CAAC,QAAgB;IACvC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,YAAY,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAClD,OAAO,YAAY,IAAI,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AACjD,CAAC;AAED;;GAEG;AACH,SAAS,YAAY,CACnB,QAAgB,EAChB,OAAe,EACf,OAAkC;IAElC,MAAM,eAAe,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC3D,MAAM,UAAU,GAAG,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC;QAC/C,CAAC,CAAC,eAAe,GAAG,OAAO;QAC3B,CAAC,CAAC,eAAe,GAAG,IAAI,GAAG,OAAO,CAAC;IACrC,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;IACvC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;QACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;IAChC,CAAC;AACH,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,QAAgB,EAChB,OAAe,EACf,OAAkC;IAElC,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;IACvC,MAAM,WAAW,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;IAE9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,qCAAqC;QACrC,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,6CAA6C;IAC7C,MAAM,eAAe,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC3D,IAAI,eAAe,KAAK,OAAO,EAAE,CAAC;QAChC,+CAA+C;QAC/C,OAAO,KAAK,CAAC;IACf,CAAC;IAED,4DAA4D;IAC5D,uEAAuE;IACvE,0EAA0E;IAC1E,gEAAgE;IAChE,MAAM,IAAI,GACR,eAAe,KAAK,KAAK,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK;QAC/C,CAAC,CAAC,MAAM;QACR,CAAC,CAAC,eAAe,CAAC;IAEtB,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;QACrB,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,IAAI,KAAK,MAAM,EAAE,CAAC;QACpB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,mBAAmB,CAAC,CAAC,CAAC;QACxE,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;QACtB,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,qCAAqC;IACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAe;QACrD;YACE,IAAI,EAAE,MAAM;YACZ,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,SAAS,WAAW,8CAA8C;YAC3E,OAAO,EAAE;gBACP,EAAE,IAAI,EAAE,sBAAsB,EAAE,KAAK,EAAE,MAAM,EAAE;gBAC/C,EAAE,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,WAAW,EAAE;gBACzC,EAAE,IAAI,EAAE,eAAe,EAAE,KAAK,EAAE,QAAQ,EAAE;gBAC1C,EAAE,IAAI,EAAE,8BAA8B,EAAE,KAAK,EAAE,UAAU,EAAE;gBAC3D,EAAE,IAAI,EAAE,mCAAmC,EAAE,KAAK,EAAE,eAAe,EAAE;gBACrE,EAAE,IAAI,EAAE,gCAAgC,EAAE,KAAK,EAAE,YAAY,EAAE;aAChE;SACF;KACF,CAAC,CAAC;IAEH,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,EAAE,CAAC,CAAC,CAAC;QACvD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;QAC1B,eAAe,GAAG,MAAM,CAAC;QACzB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,EAAE,CAAC,CAAC,CAAC;QACvD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,MAAM,KAAK,eAAe,EAAE,CAAC;QAC/B,eAAe,GAAG,OAAO,CAAC;QAC1B,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,YAAY,EAAE,CAAC;QAC5B,eAAe,GAAG,QAAQ,CAAC;QAC3B,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,SAAS,CAAC,OAAe;IACvC,EAAE,CAAC,SAAS,CAAC,OAAO,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;AAC7C,CAAC"}
+{"version":3,"file":"file-writer.js","sourceRoot":"","sources":["../../src/utils/file-writer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,QAAQ,MAAM,UAAU,CAAC;AAEhC,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAYrC,2CAA2C;AAC3C,IAAI,eAAe,GAAc,KAAK,CAAC;AAEvC,MAAM,UAAU,YAAY,CAAC,IAAe;IAC1C,eAAe,GAAG,IAAI,CAAC;AACzB,CAAC;AAED,MAAM,UAAU,YAAY;IAC1B,OAAO,eAAe,CAAC;AACzB,CAAC;AAED,8EAA8E;AAC9E,kBAAkB;AAClB,EAAE;AACF,6EAA6E;AAC7E,2EAA2E;AAC3E,6EAA6E;AAC7E,6EAA6E;AAC7E,4EAA4E;AAC5E,wBAAwB;AACxB,8EAA8E;AAE9E,kFAAkF;AAClF,IAAI,aAAa,GAAuB,IAAI,CAAC;AAC7C,gFAAgF;AAChF,IAAI,iBAAiB,GAAkB,IAAI,CAAC;AAE5C;;;;;;;;;GASG;AACH,MAAM,UAAU,oBAAoB,CAAC,GAAW;IAC9C,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,aAAa,GAAG,IAAI,CAAC;IACrB,iBAAiB,GAAG,GAAG,CAAC;IACxB,OAAO,IAAI,CAAC;AACd,CAAC;AAED,uFAAuF;AACvF,MAAM,UAAU,mBAAmB;IACjC,aAAa,GAAG,IAAI,CAAC;IACrB,iBAAiB,GAAG,IAAI,CAAC;AAC3B,CAAC;AAED,mEAAmE;AACnE,SAAS,WAAW,CAAC,OAAe;IAClC,IAAI,CAAC,aAAa,IAAI,CAAC,iBAAiB;QAAE,OAAO;IACjD,MAAM,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,iBAAiB,EAAE,OAAO,CAAC,CAAC;IACtD,mEAAmE;IACnE,IAAI,GAAG,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC;QAAE,OAAO;IACzD,aAAa,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC;AAClC,CAAC;AAED;;GAEG;AACH,SAAS,eAAe,CAAC,QAAgB;IACvC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,YAAY,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAClD,OAAO,YAAY,IAAI,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AACjD,CAAC;AAED;;GAEG;AACH,SAAS,YAAY,CACnB,QAAgB,EAChB,OAAe,EACf,OAAkC;IAElC,MAAM,eAAe,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC3D,MAAM,UAAU,GAAG,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC;QAC/C,CAAC,CAAC,eAAe,GAAG,OAAO;QAC3B,CAAC,CAAC,eAAe,GAAG,IAAI,GAAG,OAAO,CAAC;IACrC,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;IACvC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;QACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;IAChC,CAAC;AACH,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,QAAgB,EAChB,OAAe,EACf,OAAkC;IAElC,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;IACvC,MAAM,WAAW,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;IAE9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,qCAAqC;QACrC,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,WAAW,CAAC,QAAQ,CAAC,CAAC;QACtB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,6CAA6C;IAC7C,MAAM,eAAe,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC3D,IAAI,eAAe,KAAK,OAAO,EAAE,CAAC;QAChC,sEAAsE;QACtE,mEAAmE;QACnE,uEAAuE;QACvE,OAAO,KAAK,CAAC;IACf,CAAC;IAED,4DAA4D;IAC5D,uEAAuE;IACvE,0EAA0E;IAC1E,gEAAgE;IAChE,MAAM,IAAI,GACR,eAAe,KAAK,KAAK,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK;QAC/C,CAAC,CAAC,MAAM;QACR,CAAC,CAAC,eAAe,CAAC;IAEtB,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;QACrB,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,WAAW,CAAC,QAAQ,CAAC,CAAC;QACtB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,IAAI,KAAK,MAAM,EAAE,CAAC;QACpB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,mBAAmB,CAAC,CAAC,CAAC;QACxE,wEAAwE;QACxE,6DAA6D;QAC7D,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;QACtB,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,uEAAuE;QACvE,sEAAsE;QACtE,uEAAuE;QACvE,4CAA4C;QAC5C,OAAO,IAAI,CAAC;IACd,CAAC;IAED,qCAAqC;IACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAe;QACrD;YACE,IAAI,EAAE,MAAM;YACZ,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,SAAS,WAAW,8CAA8C;YAC3E,OAAO,EAAE;gBACP,EAAE,IAAI,EAAE,sBAAsB,EAAE,KAAK,EAAE,MAAM,EAAE;gBAC/C,EAAE,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,WAAW,EAAE;gBACzC,EAAE,IAAI,EAAE,eAAe,EAAE,KAAK,EAAE,QAAQ,EAAE;gBAC1C,EAAE,IAAI,EAAE,8BAA8B,EAAE,KAAK,EAAE,UAAU,EAAE;gBAC3D,EAAE,IAAI,EAAE,mCAAmC,EAAE,KAAK,EAAE,eAAe,EAAE;gBACrE,EAAE,IAAI,EAAE,gCAAgC,EAAE,KAAK,EAAE,YAAY,EAAE;aAChE;SACF;KACF,CAAC,CAAC;IAEH,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,EAAE,CAAC,CAAC,CAAC;QACvD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,WAAW,CAAC,QAAQ,CAAC,CAAC;QACtB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;QAC1B,eAAe,GAAG,MAAM,CAAC;QACzB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,gBAAgB,WAAW,EAAE,CAAC,CAAC,CAAC;QACvD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,MAAM,KAAK,eAAe,EAAE,CAAC;QAC/B,eAAe,GAAG,OAAO,CAAC;QAC1B,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACpC,IAAI,OAAO,EAAE,UAAU,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAChC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,oBAAoB,WAAW,EAAE,CAAC,CAAC,CAAC;QAC7D,WAAW,CAAC,QAAQ,CAAC,CAAC;QACtB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAM,KAAK,YAAY,EAAE,CAAC;QAC5B,eAAe,GAAG,QAAQ,CAAC;QAC3B,YAAY,CAAC,QAAQ,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;QACzC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iBAAiB,WAAW,EAAE,CAAC,CAAC,CAAC;QACxD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,SAAS,CAAC,OAAe;IACvC,EAAE,CAAC,SAAS,CAAC,OAAO,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;AAC7C,CAAC"}

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 @@
+{"version":3,"file":"manifest-prune.js","sourceRoot":"","sources":["../../src/utils/manifest-prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B,OAAO,EAAE,wBAAwB,EAAE,MAAM,2BAA2B,CAAC;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAC;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAIrC,MAAM,mBAAmB,GAAG,wBAAwB,CAAC;AACrD,MAAM,iBAAiB,GAAG,sBAAsB,CAAC;AASjD;;;;;;GAMG;AACH,SAAS,cAAc,CAAC,mBAAsC;IAC5D,MAAM,KAAK,GAAG,IAAI,GAAG,EAAU,CAAC;IAChC,KAAK,MAAM,EAAE,IAAI,mBAAmB,EAAE,CAAC;QACrC,MAAM,SAAS,GAAG,wBAAwB,CAAC,EAAE,CAAC,CAAC;QAC/C,IAAI,CAAC,SAAS;YAAE,SAAS;QACzB,KAAK,MAAM,GAAG,IAAI,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC;YACnC,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC;QAC1B,CAAC;IACH,CAAC;IACD,kEAAkE;IAClE,0EAA0E;IAC1E,sEAAsE;IACtE,KAAK,MAAM,SAAS,IAAI,gBAAgB,EAAE,EAAE,CAAC;QAC3C,IAAI,SAAS,CAAC,IAAI;YAAE,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC;QACvD,IAAI,SAAS,CAAC,EAAE;YAAE,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC;IACrD,CAAC;IAED,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;;GAMG;AACH,SAAS,kBAAkB,CAAC,GAAW;IACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,UAAU,CAAC,MAAM,CAAC,CAAC;IACnD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,OAAO,IAAI,CAAC;IACd,CAAC;IACD,IAAI,CAAC;QACH,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACnD,OAAO,CACL,OAAO,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACrC,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAC,CACpC,CAAC;IACJ,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAWD;;;;;;;;;;GAUG;AACH,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,mBAAsC,EACtC,MAAsB,EACtB,UAAwB,EAAE;IAE1B,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,IAAI,IAAI,CAAC;IACxC,MAAM,KAAK,GAAG,cAAc,CAAC,mBAAmB,CAAC,CAAC;IAClD,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,IAAI,GAAmB,EAAE,CAAC;IAEhC,KAAK,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;QACrD,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;QAC5B,oEAAoE;QACpE,+DAA+D;QAC/D,2BAA2B;QAC3B,IAAI,GAAG,CAAC,UAAU,CAAC,WAAW,CAAC,IAAI,GAAG,KAAK,UAAU,EAAE,CAAC;YACtD,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;YAClB,SAAS;QACX,CAAC;QACD,IAAI,GAAG,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;YAC9B,IAAI,kBAAkB,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;YACpB,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACnB,CAAC;YACD,SAAS;QACX,CAAC;QACD,IAAI,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;YAClB,SAAS;QACX,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACnB,CAAC;IAED,IAAI,OAAO,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjC,UAAU,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;IACxB,CAAC;IAED,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;AAClC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"template-hash.d.ts","sourceRoot":"","sources":["../../src/utils/template-hash.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAQH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAe5D;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAGnD;AAoBD;;;;;;;;GAQG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,GAAG,cAAc,CA6BtD;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,cAAc,GAAG,IAAI,CAOpE;AAED;;;;;GAKG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAQ1E;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI,CAU1E;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI,CAKlE;AAED;;GAEG;AACH,wBAAgB,UAAU,CACxB,GAAG,EAAE,MAAM,EACX,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,GACd,IAAI,CASN;AAED;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAChC,GAAG,EAAE,MAAM,EACX,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,cAAc,GACrB,OAAO,CAsBT;AAED;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CACrC,GAAG,EAAE,MAAM,EACX,YAAY,EAAE,MAAM,EACpB,eAAe,EAAE,MAAM,GACtB,OAAO,CAST;AAED;;;;;;;GAOG;AACH,wBAAgB,qBAAqB,CACnC,GAAG,EAAE,MAAM,EACX,aAAa,EAAE,MAAM,EAAE,EACvB,MAAM,EAAE,cAAc,GACrB,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAQtB;AA0ED;;;;;;;;;GASG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAwCpD"}
+{"version":3,"file":"template-hash.d.ts","sourceRoot":"","sources":["../../src/utils/template-hash.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAOH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAe5D;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAGnD;AAoBD;;;;;;;;GAQG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,GAAG,cAAc,CA6BtD;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,cAAc,GAAG,IAAI,CAOpE;AAED;;;;;GAKG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAQ1E;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI,CAU1E;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI,CAKlE;AAED;;GAEG;AACH,wBAAgB,UAAU,CACxB,GAAG,EAAE,MAAM,EACX,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,GACd,IAAI,CASN;AAED;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAChC,GAAG,EAAE,MAAM,EACX,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,cAAc,GACrB,OAAO,CAsBT;AAED;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CACrC,GAAG,EAAE,MAAM,EACX,YAAY,EAAE,MAAM,EACpB,eAAe,EAAE,MAAM,GACtB,OAAO,CAST;AAED;;;;;;;GAOG;AACH,wBAAgB,qBAAqB,CACnC,GAAG,EAAE,MAAM,EACX,aAAa,EAAE,MAAM,EAAE,EACvB,MAAM,EAAE,cAAc,GACrB,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAQtB;AA8DD,oDAAoD;AACpD,MAAM,WAAW,uBAAuB;IACtC;;;;;;;;OAQG;IACH,YAAY,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IACnC;;;;;OAKG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,gBAAgB,CAC9B,GAAG,EAAE,MAAM,EACX,OAAO,GAAE,uBAA4B,GACpC,MAAM,CAyDR"}