@pennixrv/trellis 0.7.1-beta.0 → 0.7.1-beta.2

package/dist/templates/extract.js.map

@@ -1 +1 @@
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+{"version":3,"file":"extract.js","sourceRoot":"","sources":["../../src/templates/extract.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAAE,4BAA4B,EAAE,MAAM,4BAA4B,CAAC;AAE1E,MAAM,UAAU,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAClD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;AAI3C;;GAEG;AACH,MAAM,UAAU,sBAAsB;IACpC,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACrD,IAAI,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QAChC,OAAO,YAAY,CAAC;IACtB,CAAC;IACD,MAAM,IAAI,KAAK,CACb,4EAA4E,CAC7E,CAAC;AACJ,CAAC;AAED,wDAAwD;AACxD,MAAM,UAAU,oBAAoB;IAClC,OAAO,sBAAsB,EAAE,CAAC;AAClC,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB;IACnC,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IACpD,IAAI,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QAChC,OAAO,YAAY,CAAC;IACtB,CAAC;IACD,MAAM,IAAI,KAAK,CACb,0EAA0E,CAC3E,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,uBAAuB;IACrC,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,UAAU,CAAC,CAAC;IACtD,IAAI,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QAChC,OAAO,YAAY,CAAC;IACtB,CAAC;IACD,MAAM,IAAI,KAAK,CACb,8EAA8E,CAC/E,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,iBAAiB;IAC/B,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;IAChD,IAAI,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QAChC,OAAO,YAAY,CAAC;IACtB,CAAC;IACD,MAAM,IAAI,KAAK,CACb,kEAAkE,CACnE,CAAC;AACJ,CAAC;AAED,mDAAmD;AACnD,MAAM,UAAU,eAAe;IAC7B,OAAO,iBAAiB,EAAE,CAAC;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,eAAe,CAAC,YAAoB;IAClD,MAAM,WAAW,GAAG,oBAAoB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;IACtD,OAAO,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;AAC5C,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,YAAY,CAC1B,QAA0B,EAC1B,QAAgB;IAEhB,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAC;IAC9D,OAAO,EAAE,CAAC,YAAY,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;AAChD,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,YAAoB;IAC7C,OAAO,eAAe,CAAC,WAAW,YAAY,EAAE,CAAC,CAAC;AACpD,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,YAAoB;IAC/C,OAAO,eAAe,CAAC,YAAY,CAAC,CAAC;AACvC,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,QAAgB;IAC1C,OAAO,YAAY,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;AAC5C,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,eAAuB,EACvB,QAAgB,EAChB,OAAkC;IAElC,MAAM,WAAW,GAAG,oBAAoB,EAAE,CAAC;IAC3C,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,eAAe,CAAC,CAAC;IACxD,MAAM,gBAAgB,CAAC,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;AACrD,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,GAAW,EACX,IAAY,EACZ,OAAkC;IAElC,SAAS,CAAC,IAAI,CAAC,CAAC;IAEhB,KAAK,MAAM,KAAK,IAAI,EAAE,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC;QACxC,IACE,KAAK,KAAK,aAAa;YACvB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAC9C,CAAC;YACD,SAAS;QACX,CAAC;QACD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;QACtC,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;QAElC,IAAI,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;YACvB,MAAM,gBAAgB,CAAC,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;QACrD,CAAC;aAAM,CAAC;YACN,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAClD,MAAM,YAAY,GAChB,OAAO,EAAE,UAAU,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC;YAC1E,MAAM,SAAS,CAAC,QAAQ,EAAE,4BAA4B,CAAC,OAAO,CAAC,EAAE;gBAC/D,UAAU,EAAE,YAAY;aACzB,CAAC,CAAC;QACL,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/utils/manifest-prune.d.ts

@@ -14,7 +14,8 @@
  * self-correct on the next routine command.
  *
  * Rules:
- *   - `.trellis/*` entries are ALWAYS kept. `trellis uninstall` removes
+ *   - `.trellis/*` entries are kept unless an explicitly retired file is missing.
+ *     `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.

package/dist/utils/manifest-prune.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest-prune.d.ts","sourceRoot":"","sources":["../../src/utils/manifest-prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAWH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAE5D,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"}
+{"version":3,"file":"manifest-prune.d.ts","sourceRoot":"","sources":["../../src/utils/manifest-prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AAWH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAE5D,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,CA0Cb"}

package/dist/utils/manifest-prune.js

@@ -14,7 +14,8 @@
  * self-correct on the next routine command.
  *
  * Rules:
- *   - `.trellis/*` entries are ALWAYS kept. `trellis uninstall` removes
+ *   - `.trellis/*` entries are kept unless an explicitly retired file is missing.
+ *     `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.
@@ -101,15 +102,21 @@ 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 (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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package/dist/utils/template-hash.d.ts

@@ -116,10 +116,10 @@ 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.js

@@ -265,10 +265,10 @@ 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 +294,19 @@ 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.2",
   "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.2"
   },
   "devDependencies": {
     "@eslint/js": "^9.18.0",