Complete graph phases 0-2 and enforce zero-warning lint

.oxlintrc.json

@@ -196,6 +196,12 @@
         "threadnote/no-effect-runtime": "off"
       }
     },
+    {
+      "files": ["test/helpers/node-*.ts"],
+      "rules": {
+        "effecttsgo/node-builtin-import": "off"
+      }
+    },
     {
       "files": ["test/**/*.test.ts", "test/**/*.spec.ts", "test/e2e/**/*.e2e.ts"],
       "rules": {

.oxlintrc.max-lines.json

@@ -3,19 +3,10 @@
   "categories": {
     "correctness": "off"
   },
-  "ignorePatterns": [
-    "src/code_graph/build_status.ts",
-    "src/code_graph/indexer.ts",
-    "src/code_graph/inventory.ts",
-    "src/manager_graph.tsx",
-    "src/mcp_server.ts",
-    "src/memory.ts",
-    "website/src/content/docs.ts"
-  ],
   "plugins": [],
   "rules": {
     "max-lines": [
-      "warn",
+      "error",
       {
         "max": 2000,
         "skipBlankLines": false,

.oxlintrc.strict.json

@@ -70,6 +70,12 @@
         "threadnote/no-effect-runtime": "off"
       }
     },
+    {
+      "files": ["test/helpers/node-*.ts"],
+      "rules": {
+        "effecttsgo/node-builtin-import": "off"
+      }
+    },
     {
       "files": ["test/**/*.test.ts", "test/**/*.spec.ts", "test/e2e/**/*.e2e.ts"],
       "rules": {

README.md

@@ -236,11 +236,17 @@ threadnote graph repair --all --dry-run
 threadnote graph compact --dry-run
 ```
 
-`graph status` reports active SQLite database, WAL, and SHM bytes plus page/freelist and reclaimable-byte diagnostics.
-When both 512 MiB and 20% of the database are reclaimable it recommends explicit compaction. `graph compact` takes
-zero-wait maintenance and checkout locks, verifies the active snapshot before and after SQLite's transactional
-`VACUUM`, and defers safely during a build. Preview it with `--dry-run`; `--force` is available below the reviewed
-threshold.
+`graph status` reports physical SQLite database, WAL, and SHM bytes separately from pages in use and freelist bytes
+already reusable inside the database. A large physical file can therefore contain little live graph data without
+causing future writes to grow it. When freelist bytes are both at least 512 MiB and 20% of the database, a running
+Manager automatically compacts one eligible database at a time after active builders release their locks and sufficient
+disk headroom is verified. SQLite can require more than twice the database size as temporary free space during `VACUUM`, so Manager
+withholds compaction when that conservative headroom cannot be proved. Automatic compaction runs in an isolated child
+process, keeping Manager responsive; Manager shows the latest check, deferral, failure, or reclaimed bytes. Structural
+fragmentation analysis can scan live SQLite pages, so it is never scheduled automatically. Compaction rechecks the
+active snapshot before and after the transactional rewrite, and interruption leaves the original database intact.
+`graph compact --dry-run` remains available to inspect additional fragmentation explicitly, choose the timing, or
+troubleshoot; `--force` is the expert override below the reviewed threshold.
 
 `graph diagnostics` is home-wide and does not resolve a repository from the current directory. It reports every local
 graph database, ready snapshot, indexed view, active build, waiter, storage total, health issue, and obsolete store;
@@ -260,6 +266,8 @@ before acting. The CLI equivalent for an orphaned store is
 
 `threadnote manage` fails fast when graph repair or another native graph maintenance operation is already active;
 an already-running Manager returns an explicit busy response for graph requests until maintenance finishes.
+Manager labels graph views with repository name, the branch observed at a stated boundary, and trusted local folder whenever available; opaque
+checkout and worktree identities are reserved for last-resort diagnostics and exact CLI targeting.
 
 Maven, Gradle, Kotlin Multiplatform/Android conventions, SwiftPM, conservative Xcode metadata, and nested or integrated
 Bazel workspaces form a static workspace model; repository build scripts are never executed. Bazel `WORKSPACE`,

THIRD_PARTY.md

@@ -15,6 +15,7 @@ Direct runtime software and packages bundled into the published JavaScript retai
 - `remark-gfm` (MIT)
 - `three` (MIT), used for GPU-accelerated manager graph rendering
 - `js-yaml` (MIT)
+- `yaml` 2.9.0 (ISC), used for comment-preserving Manager Workset manifest updates
 - TypeScript compiler 5.9 (`typescript-compiler`, Apache-2.0), bundled for native TypeScript/JavaScript graph extraction
 - `fflate` 0.8.2 (MIT), used for bounded local text extraction from tracked OpenXML, OpenDocument, and EPUB archives
 - `unpdf` 1.6.2 (MIT) and its bundled PDF.js engine (Apache-2.0), used for local tracked-PDF text and link extraction
@@ -42,6 +43,19 @@ Grammar and parser license copies, source revisions, ABIs, and SHA-256 checksums
 pinned MIT-licensed BGE Small embedding model is installed automatically by `threadnote install`; other model files
 require an explicit `threadnote models install` action. Catalog entries identify every model source and license.
 
+### `yaml` 2.9.0 license notice
+
+Copyright Eemeli Aro <eemeli@gmail.com>
+
+Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby
+granted, provided that the above copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN
+AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THIS SOFTWARE.
+
 ## Public website
 
 The separately deployed GitHub Pages website is not part of the standalone release. Its build uses Vite and