@pennixrv/trellis 0.7.1-beta.0 → 0.7.1-beta.10

package/dist/utils/manifest-prune.js

@@ -14,7 +14,10 @@
  * self-correct on the next routine command.
  *
  * Rules:
- *   - `.trellis/*` entries are ALWAYS kept. `trellis uninstall` removes
+ *   - `.trellis/*` entries are kept unless excluded from template tracking
+ *     (user data, runtime state, caches) or an explicitly retired file is missing.
+ *     Existing registry-managed spec baselines are retained.
+ *     `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.
@@ -35,7 +38,7 @@ 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 { isRuntimeHashPath, saveHashes, shouldExcludeFromHash } from "./template-hash.js";
 import { toPosix } from "./posix.js";
 import { TRELLIS_BLOCK_END, TRELLIS_BLOCK_START } from "./managed-paths.js";
 /**
@@ -101,15 +104,23 @@ function shouldKeepAgentsMd(cwd) {
 export function pruneOrphanManifestKeys(cwd, configuredPlatforms, hashes, options = {}) {
     const persist = options.persist ?? true;
     const known = buildKnownKeys(configuredPlatforms);
+    const retired = new Set(getAllMigrations()
+        .filter((migration) => migration.type === "safe-file-delete")
+        .map((migration) => toPosix(migration.from)));
     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.
+        // Missing retired files no longer need a modified-file baseline.
         if (key.startsWith(".trellis/") || key === ".trellis") {
-            kept[key] = value;
+            if (isRuntimeHashPath(key) ||
+                (shouldExcludeFromHash(key) && !key.startsWith(".trellis/spec/")) ||
+                (retired.has(key) && !fs.existsSync(path.join(cwd, key)))) {
+                pruned.push(key);
+            }
+            else {
+                kept[key] = value;
+            }
             continue;
         }
         if (key === FILE_NAMES.AGENTS) {

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

@@ -1 +1 @@
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+{"version":3,"file":"manifest-prune.js","sourceRoot":"","sources":["../../src/utils/manifest-prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkCG;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,iBAAiB,EAAE,UAAU,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC1F,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AACrC,OAAO,EAAE,iBAAiB,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAW5E;;;;;;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,OAAO,GAAG,IAAI,GAAG,CACrB,gBAAgB,EAAE;SACf,MAAM,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,SAAS,CAAC,IAAI,KAAK,kBAAkB,CAAC;SAC5D,GAAG,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAC/C,CAAC;IACF,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,iEAAiE;QACjE,IAAI,GAAG,CAAC,UAAU,CAAC,WAAW,CAAC,IAAI,GAAG,KAAK,UAAU,EAAE,CAAC;YACtD,IACE,iBAAiB,CAAC,GAAG,CAAC;gBACtB,CAAC,qBAAqB,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,gBAAgB,CAAC,CAAC;gBACjE,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,EACzD,CAAC;gBACD,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;YACpB,CAAC;YACD,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

@@ -86,6 +86,7 @@ export declare function getModificationStatus(cwd: string, relativePaths: string
 /**
  * Check if a path should be excluded from hash tracking
  */
+export declare function isRuntimeHashPath(relativePath: string): boolean;
 export declare function shouldExcludeFromHash(relativePath: string): boolean;
 /** Options accepted by {@link initializeHashes}. */
 export interface InitializeHashesOptions {
@@ -116,10 +117,10 @@ export interface InitializeHashesOptions {
  * where a blind directory walk of `.codex/` / `.claude/` swept up
  * user-owned runtime data (chat history, session JSONLs).
  *
- * `.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).
+ * On first init, `.trellis/` is walked recursively (with
+ * `EXCLUDE_FROM_HASH`) to seed update tracking. Re-init merges only the
+ * platform paths written in that run, preserving existing workflow/config
+ * hashes so local edits remain visible to `trellis update`.
  *
  * @returns Number of files hashed in the final manifest.
  */

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;AAOH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAgB5D;;;;;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;AAiBD;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAQnE;AAkCD,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"}
+{"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;AAgB5D;;;;;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;AAiBD;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAM/D;AAED,wBAAgB,qBAAqB,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CASnE;AAkCD,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"}

package/dist/utils/template-hash.js

@@ -220,8 +220,15 @@ const EXCLUDE_FROM_HASH = [
 /**
  * Check if a path should be excluded from hash tracking
  */
+export function isRuntimeHashPath(relativePath) {
+    const normalizedPath = toPosix(relativePath);
+    return (/(^|\/)(?:\.runtime|__pycache__|session-handoffs)(\/|$)/.test(normalizedPath) ||
+        normalizedPath.endsWith(".pyc"));
+}
 export function shouldExcludeFromHash(relativePath) {
     const normalizedPath = toPosix(relativePath);
+    if (isRuntimeHashPath(normalizedPath))
+        return true;
     for (const pattern of EXCLUDE_FROM_HASH) {
         if (normalizedPath.includes(pattern)) {
             return true;
@@ -265,10 +272,10 @@ function collectFiles(cwd, dir) {
  * where a blind directory walk of `.codex/` / `.claude/` swept up
  * user-owned runtime data (chat history, session JSONLs).
  *
- * `.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).
+ * On first init, `.trellis/` is walked recursively (with
+ * `EXCLUDE_FROM_HASH`) to seed update tracking. Re-init merges only the
+ * platform paths written in that run, preserving existing workflow/config
+ * hashes so local edits remain visible to `trellis update`.
  *
  * @returns Number of files hashed in the final manifest.
  */
@@ -294,19 +301,19 @@ export function initializeHashes(cwd, options = {}) {
             }
         }
     }
-    // .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);
-        try {
-            const content = fs.readFileSync(fullPath, "utf-8");
-            hashes[relativePath] = computeHash(content);
-        }
-        catch {
-            // Skip files that can't be read (binary, etc.)
+    // Re-init only adds platform files. Re-walking `.trellis/` would bless
+    // customized workflow/config content and let the next update overwrite it.
+    if (!merge) {
+        const files = collectFiles(cwd, ".trellis");
+        for (const relativePath of files) {
+            const fullPath = path.join(cwd, relativePath);
+            try {
+                const content = fs.readFileSync(fullPath, "utf-8");
+                hashes[relativePath] = computeHash(content);
+            }
+            catch {
+                // Skip files that can't be read (binary, etc.)
+            }
         }
     }
     // Backwards-compat path: when `trackedPaths` is not supplied (callers that

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@pennixrv/trellis",
-  "version": "0.7.1-beta.0",
+  "version": "0.7.1-beta.10",
   "description": "AI capabilities grow like ivy — Trellis provides the structure to guide them along a disciplined path",
   "type": "module",
   "main": "./dist/index.js",
@@ -34,7 +34,7 @@
     "inquirer": "^9.3.7",
     "undici": "^6.21.0",
     "zod": "^4.4.2",
-    "@pennixrv/trellis-core": "0.7.1-beta.0"
+    "@pennixrv/trellis-core": "0.7.1-beta.10"
   },
   "devDependencies": {
     "@eslint/js": "^9.18.0",