Threadnote 4.0.0

.github/dependabot.yml

@@ -3,7 +3,7 @@
 
 version: 2
 updates:
-  - package-ecosystem: npm
+  - package-ecosystem: bun
     directory: /
     schedule:
       interval: weekly

.github/release-notes/v4.0.0-beta.10.md

@@ -0,0 +1,24 @@
+## What's new
+
+Threadnote 4 beta.10 makes migration from Threadnote 3 reliable when the new home already contains generated state or
+a local shared-memory repository has unpublished work.
+
+- Migrate without false conflicts between the legacy and current update-check caches.
+- Preserve unpublished local share commits, branch refs, Git objects, configuration, and worktree content.
+- Ignore only transient `FETCH_HEAD` bookkeeping that can change while Git checks a shared-memory remote.
+- Keep the complete legacy `~/.openviking` home unchanged as the rollback source.
+
+If migration stopped on `update-check.json` or a share `FETCH_HEAD` with beta.9:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.10/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.11.md

@@ -0,0 +1,26 @@
+## What's new
+
+Threadnote 4 beta.11 lets recovery finish when an earlier beta has already updated a canonical memory or resource after
+it was copied from the preserved Threadnote 3 home.
+
+- Keep the current `~/.threadnote/data/` copy when it differs from the older `~/.openviking` rollback copy.
+- Continue recovering disjoint legacy memories and resources, and record how many current entries were preserved.
+- Still stop safely on different non-canonical settings or metadata instead of overwriting them.
+- Keep the complete legacy `~/.openviking` home unchanged as the rollback source.
+- Add privacy-safe local production diagnostics that retain complete history on Windows, plus an approval-gated GitHub
+  issue preview workflow.
+
+If beta.10 stopped on `Recovery would overwrite different existing content`:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.11/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.12.md

@@ -0,0 +1,25 @@
+## What's new
+
+Threadnote 4 beta.12 lets interrupted home recovery finish when a local shared-memory repository changed transient Git
+bookkeeping between migration attempts.
+
+- Ignore legacy `COMMIT_EDITMSG`, `FETCH_HEAD`, `gc.log`, and Git-generated lockfiles inside managed share gitdirs.
+- Preserve the current beta copy when its transient commit message differs from the legacy rollback source.
+- Continue copying and verifying unpublished branch refs, commit objects, `ORIG_HEAD`, configuration, the index,
+  reflogs, and worktree content.
+- Keep the complete legacy `~/.openviking` home unchanged as the rollback source.
+
+If beta.11 stopped on a managed share gitdir conflict:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.12/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.13.md

@@ -0,0 +1,24 @@
+## What's new
+
+Threadnote 4 beta.13 completes interrupted local-share recovery when the active beta repository has refreshed or
+changed its Git index since the legacy home was copied.
+
+- Keep the current `~/.threadnote` managed-share index, including its staging state.
+- Leave the legacy index unchanged under `~/.openviking` as rollback evidence.
+- Continue recovering disjoint legacy memories and unpublished Git objects.
+- Still fail closed on different refs, configuration, reflogs, operation state, or other durable Git content.
+
+If beta.12 stopped on `share/teams/<team>.gitdir/index`:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.13/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.14.md

@@ -0,0 +1,25 @@
+## What's new
+
+Threadnote 4 beta.14 makes interrupted home recovery safe for the complete state of an active local shared-memory
+repository, rather than handling individual Git files one at a time.
+
+- Keep the current `~/.threadnote` share checkout as one unit, including staged changes, unpublished objects, refs,
+  reflogs, configuration, and in-progress Git operations.
+- Never combine current and legacy repository internals into a potentially invalid hybrid checkout.
+- Leave the complete legacy repository unchanged under `~/.openviking` as rollback evidence.
+- Stop before copying when the current checkout is incomplete, unsafe, or points at a different Git directory.
+
+If an earlier beta stopped on a path under `share/teams/<team>.gitdir/`:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.14/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.15.md

@@ -0,0 +1,27 @@
+## What's new
+
+Threadnote 4 beta.15 resumes shared-memory migrations that an earlier beta interrupted after copying only part of a
+Git checkout.
+
+- Complete a partial checkout only when every durable file is proven to come from the unchanged legacy repository.
+- Preserve staged changes, unpublished objects, refs, reflogs, and unknown Git state by stopping when either copy has
+  genuinely diverged.
+- Ignore and clean transient Git operation files and locks without weakening checks for durable repository data.
+- Serialize migration with agent share activity, stage missing files outside the repository, verify them, and install
+  them atomically.
+- Keep `~/.openviking` unchanged as the rollback source throughout recovery.
+
+For the developer whose beta.14 migration reported an incomplete or unsafe managed share checkout:
+
+```bash
+threadnote update --beta
+threadnote migrate --apply
+threadnote doctor
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.15/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.16.md

@@ -0,0 +1,37 @@
+## What's new
+
+Threadnote 4 beta.16 adds a self-contained, worktree-aware code graph for precise source navigation without Graphify,
+Python, a daemon, or a copied graph directory.
+
+- Search current source through the dedicated `inspect_code_graph` MCP tool instead of mixing code evidence into memory
+  recall.
+- Use `threadnote graph query`, `explain`, `path`, and `impact` for symbols, relationships, dependency paths, and
+  change-impact analysis.
+- Keep graph snapshots current during MCP sessions with one deduplicated watcher per inspected worktree; one-shot CLI
+  commands synchronously refresh stale indexes.
+- Store derived graph data under `~/.threadnote/indexes/code-graph` in SQLite, with optional semantic associations
+  produced by Threadnote's installed local embedding model.
+- Isolate dirty overlays between linked worktrees, share immutable committed facts safely, and materialize the exact
+  requested Git base for deleted-code impact analysis.
+- Add bounded indexing, traversal, export, repair, and purge operations with stored quality and performance baselines.
+
+To build and inspect the graph explicitly:
+
+```bash
+threadnote graph index
+threadnote graph query --query "where is recall freshness decided"
+threadnote graph impact --base origin/main
+```
+
+Existing beta installations can update in place:
+
+```bash
+threadnote update --beta
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.16/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.17.md

@@ -0,0 +1,39 @@
+## What's new
+
+Threadnote 4 beta.17 adds a self-contained, worktree-aware code graph for precise source navigation without Graphify,
+Python, a daemon, or a copied graph directory.
+
+- Search current source through the dedicated `inspect_code_graph` MCP tool instead of mixing code evidence into memory
+  recall.
+- Use `threadnote graph query`, `explain`, `path`, and `impact` for symbols, relationships, dependency paths, and
+  change-impact analysis.
+- Keep graph snapshots current during MCP sessions with one deduplicated watcher per inspected worktree; one-shot CLI
+  commands synchronously refresh stale indexes.
+- Store derived graph data under `~/.threadnote/indexes/code-graph` in SQLite, with optional semantic associations
+  produced by Threadnote's installed local embedding model.
+- Isolate dirty overlays between linked worktrees, share immutable committed facts safely, and materialize the exact
+  requested Git base for deleted-code impact analysis.
+- Add bounded indexing, traversal, export, repair, and purge operations with stored quality and performance baselines.
+- Keep machine-readable command output clean when llama.cpp reports model compatibility notices during semantic graph
+  search.
+
+To build and inspect the graph explicitly:
+
+```bash
+threadnote graph index
+threadnote graph query --query "where is recall freshness decided"
+threadnote graph impact --base origin/main
+```
+
+Existing beta installations can update in place:
+
+```bash
+threadnote update --beta
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.17/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.18.md

@@ -0,0 +1,41 @@
+## What's new
+
+Threadnote 4 beta.18 adds a self-contained, worktree-aware code graph for precise source navigation without Graphify,
+Python, a daemon, or a copied graph directory.
+
+- Search current source through the dedicated `inspect_code_graph` MCP tool instead of mixing code evidence into memory
+  recall.
+- Use `threadnote graph query`, `explain`, `path`, and `impact` for symbols, relationships, dependency paths, and
+  change-impact analysis.
+- Keep graph snapshots current during MCP sessions with one deduplicated watcher per inspected worktree; one-shot CLI
+  commands synchronously refresh stale indexes.
+- Store derived graph data under `~/.threadnote/indexes/code-graph` in SQLite, with optional semantic associations
+  produced by Threadnote's installed local embedding model.
+- Isolate dirty overlays between linked worktrees, share immutable committed facts safely, and materialize the exact
+  requested Git base for deleted-code impact analysis.
+- Add bounded indexing, traversal, export, repair, and purge operations with stored quality and performance baselines.
+- Keep machine-readable command output clean when llama.cpp reports model compatibility notices during semantic graph
+  search.
+- Verify packaged JSON commands using their real stdout contract on every release platform without conflating stderr
+  diagnostics with the machine-readable payload.
+
+To build and inspect the graph explicitly:
+
+```bash
+threadnote graph index
+threadnote graph query --query "where is recall freshness decided"
+threadnote graph impact --base origin/main
+```
+
+Existing beta installations can update in place:
+
+```bash
+threadnote update --beta
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.18/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.19.md

@@ -0,0 +1,43 @@
+## What's new
+
+Threadnote 4 beta.19 adds a self-contained, worktree-aware code graph for precise source navigation without Graphify,
+Python, a daemon, or a copied graph directory.
+
+- Search current source through the dedicated `inspect_code_graph` MCP tool instead of mixing code evidence into memory
+  recall.
+- Use `threadnote graph query`, `explain`, `path`, and `impact` for symbols, relationships, dependency paths, and
+  change-impact analysis.
+- Keep graph snapshots current during MCP sessions with one deduplicated watcher per inspected worktree; one-shot CLI
+  commands synchronously refresh stale indexes.
+- Store derived graph data under `~/.threadnote/indexes/code-graph` in SQLite, with optional semantic associations
+  produced by Threadnote's installed local embedding model.
+- Isolate dirty overlays between linked worktrees, share immutable committed facts safely, and materialize the exact
+  requested Git base for deleted-code impact analysis.
+- Add bounded indexing, traversal, export, repair, and purge operations with stored quality and performance baselines.
+- Keep machine-readable command output clean when llama.cpp reports model compatibility notices during semantic graph
+  search.
+- Preserve completed semantic matches when inference crosses the graph traversal time budget, return them as partial
+  evidence, and skip only subsequent expansion work.
+- Verify packaged JSON commands using their real stdout contract on every release platform without conflating stderr
+  diagnostics with the machine-readable payload.
+
+To build and inspect the graph explicitly:
+
+```bash
+threadnote graph index
+threadnote graph query --query "where is recall freshness decided"
+threadnote graph impact --base origin/main
+```
+
+Existing beta installations can update in place:
+
+```bash
+threadnote update --beta
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.19/scripts/install.sh |
+  sh -s -- --beta
+```

.github/release-notes/v4.0.0-beta.20.md

@@ -0,0 +1,39 @@
+## What's new
+
+Threadnote 4 beta.20 removes the aggregate source-byte ceiling from the native code graph so large monorepos can be
+indexed without recreating Graphify's monolithic-graph limit.
+
+- Parse uncached source into the SQLite-backed fact cache in bounded, resumable batches, releasing ordinary source text
+  after every batch instead of retaining the repository in memory.
+- Replace raw package and TypeScript configuration retention with compact, bounded resolution metadata while preserving
+  package attribution, path aliases, workspace dependencies, and cross-package calls.
+- Treat a Git checkout as one integrated graph scope: nested apps and packages use their deepest local package and
+  TypeScript configuration while still resolving into the surrounding monorepo workspace.
+- Enforce file and graph-cardinality limits before expensive dirty-overlay work, count cached facts before
+  materialization, and clean abandoned parser-cache rows after failed builds and repair.
+- Preserve the last ready snapshot when a later batch fails, prune exact stale cache revisions, and make forced rebuilds
+  replace corrupted cached parser facts from source.
+- Expose CLI parity through the MCP `inspect_code_graph` tool: `query`, `explain`, `path`, and `impact` are all available,
+  and impact can derive its seeds from a Git `base` when no explicit query is supplied.
+- Expand release tests with a real Git inventory above the former 128 MiB limit, 129-file committed and dirty batch
+  boundaries, nested monorepo resolution, cache cleanup, full rebuild, MCP Git-base impact, and packaged-binary checks.
+
+To inspect a large workspace:
+
+```bash
+threadnote graph query --query "BaseHydrationManager"
+threadnote graph impact --base origin/main
+```
+
+Existing beta installations can update in place:
+
+```bash
+threadnote update --beta
+```
+
+Fresh beta installation:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Kashkovsky/threadnote/v4.0.0-beta.20/scripts/install.sh |
+  sh -s -- --beta
+```