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

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

@@ -1 +1 @@
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package/dist/utils/template-hash.js

@@ -16,7 +16,6 @@ import { createHash } from "node:crypto";
 import fs from "node:fs";
 import path from "node:path";
 import { DIR_NAMES, FILE_NAMES } from "../constants/paths.js";
-import { ALL_MANAGED_DIRS } from "../configurators/index.js";
 import { toPosix } from "./posix.js";
 /** File name for storing template hashes */
 const HASHES_FILE = ".template-hashes.json";
@@ -204,13 +203,7 @@ export function getModificationStatus(cwd, relativePaths, hashes) {
     return result;
 }
 /**
- * Directories to scan for template files during init (derived from platform registry)
- */
-const TEMPLATE_DIRS = ALL_MANAGED_DIRS;
-/** Root-level template files written by init and managed by update. */
-const TEMPLATE_FILES = [FILE_NAMES.AGENTS];
-/**
- * Patterns to exclude from hash tracking
+ * Patterns to exclude from hash tracking (only applied to the .trellis/ walk).
  */
 const EXCLUDE_FROM_HASH = [
     ".template-hashes.json", // Hash file itself
@@ -241,7 +234,7 @@ function shouldExcludeFromHash(relativePath) {
  * Returned paths are POSIX-normalized so they can be used directly as
  * hash dictionary keys regardless of host OS.
  */
-function collectFiles(cwd, dir, relativeTo = "") {
+function collectFiles(cwd, dir) {
     const fullDir = path.join(cwd, dir);
     if (!fs.existsSync(fullDir)) {
         return [];
@@ -254,7 +247,7 @@ function collectFiles(cwd, dir, relativeTo = "") {
             continue;
         }
         if (entry.isDirectory()) {
-            files.push(...collectFiles(cwd, relativePath, relativeTo));
+            files.push(...collectFiles(cwd, relativePath));
         }
         else if (entry.isFile()) {
             files.push(toPosix(relativePath));
@@ -265,23 +258,48 @@ function collectFiles(cwd, dir, relativeTo = "") {
 /**
  * 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 function initializeHashes(cwd) {
-    const hashes = {};
-    for (const relativePath of TEMPLATE_FILES) {
-        if (shouldExcludeFromHash(relativePath)) {
-            continue;
+export function initializeHashes(cwd, options = {}) {
+    const { trackedPaths, merge = false } = options;
+    const hashes = merge ? loadHashes(cwd) : {};
+    // Platform + root files: hash only paths actually written this run.
+    if (trackedPaths) {
+        for (const relativePath of trackedPaths) {
+            // `.trellis/` paths are handled by the walk below — don't double-track.
+            if (relativePath.startsWith(".trellis/") || relativePath === ".trellis") {
+                continue;
+            }
+            const fullPath = path.join(cwd, ...relativePath.split("/"));
+            if (!fs.existsSync(fullPath))
+                continue;
+            try {
+                const content = fs.readFileSync(fullPath, "utf-8");
+                hashes[toPosix(relativePath)] = computeHash(content);
+            }
+            catch {
+                // Skip files that can't be read (binary, etc.)
+            }
         }
+    }
+    // .trellis/ workflow tree: still walked recursively. Accuracy here is for
+    // `trellis update`'s 3-way merge of workflow.md / config.yaml / scripts;
+    // uninstall removes .trellis/ wholesale so it does not matter for the
+    // data-loss bug this contract addresses.
+    const files = collectFiles(cwd, ".trellis");
+    for (const relativePath of files) {
         const fullPath = path.join(cwd, relativePath);
-        if (!fs.existsSync(fullPath)) {
-            continue;
-        }
         try {
             const content = fs.readFileSync(fullPath, "utf-8");
             hashes[relativePath] = computeHash(content);
@@ -290,19 +308,23 @@ export function initializeHashes(cwd) {
             // Skip files that can't be read (binary, etc.)
         }
     }
-    // Collect all template files
-    for (const dir of TEMPLATE_DIRS) {
-        const files = collectFiles(cwd, dir);
-        for (const relativePath of files) {
-            // `relativePath` is POSIX (collectFiles normalizes); reconstruct an
-            // OS-native path for the actual fs read.
+    // Backwards-compat path: when `trackedPaths` is not supplied (callers that
+    // haven't been updated yet), keep tracking root-level files that exist on
+    // disk. This preserves the legacy behavior for tests / scripts that don't
+    // go through the new recording flow.
+    if (!trackedPaths) {
+        for (const relativePath of [FILE_NAMES.AGENTS]) {
+            if (shouldExcludeFromHash(relativePath))
+                continue;
             const fullPath = path.join(cwd, relativePath);
+            if (!fs.existsSync(fullPath))
+                continue;
             try {
                 const content = fs.readFileSync(fullPath, "utf-8");
-                hashes[relativePath] = computeHash(content);
+                hashes[toPosix(relativePath)] = computeHash(content);
             }
             catch {
-                // Skip files that can't be read (binary, etc.)
+                // Skip
             }
         }
     }

package/dist/utils/template-hash.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mindfoldhq/trellis",
-  "version": "0.6.0-beta.10",
+  "version": "0.6.0-beta.12",
   "description": "AI capabilities grow like ivy — Trellis provides the structure to guide them along a disciplined path",
   "type": "module",
   "main": "./dist/index.js",