v1.13.12: skills audit + token-tracking fix + codecontext + cap50 + UI cleanups

Multi-topic batch. The big-ticket item is the skills audit; the rest are
smaller patches that compounded during the audit work.

## Skills audit (rules→recipes split)

Vendored all 26 skills from /home/samkintop/opt/skills/ into data/skills/
(the boocode-repo-local skill library — see docker-compose change below).
Audited via 5 parallel Claude Code agent-teams running the
mgechev/skills-best-practices 4-step protocol (Discovery → Logic → Edge
Case → self-Architecture-Refinement) per skill, ~2 min wall-clock vs the
~3.7-hour serial estimate.

Result: 14 skills surviving (renamed to gerund form, frontmatter matched),
11 deleted (duplicates, BooCode-irrelevant patterns, Claude-already-does-
natively), 1 migrated to BOOCHAT.md/BOOCODER.md as an always-true rule
(verification-before-completion). Each surviving skill had its description
refined to fix specific trigger gaps surfaced by the protocol — 4
real-bug findings landed (dead refs, stale tags, broken sub-file
references in the original vendored content).

Audit decisions documented in openspec/changes/v1.13.12-skills-audit/
audit-notes.md. Convention codified in BOOCHAT.md/BOOCODER.md "rules vs
recipes" sections — future workflow rules go to those files (100%
present), recipes stay in data/skills/ (~6% invoke rate in multi-turn
per the Codeminer42 measurement).

## Token tracking + stale-stream banner fix (same root cause)

ws-frames.ts IsoTimestamp was z.string().min(1) but postgres returns
timestamp columns as JS Date objects. Every message_complete /
session_updated / chat_updated frame was failing the v1.13.11 Zod gate
and being silently dropped. Symptoms: token tracking blank in the UI
(no usage frames landed); the 60s no-token-activity timer tripped the
stale-stream banner because the frontend's local message state never
saw status='streaming' flip to 'complete'.

Fix: z.preprocess(v => v instanceof Date ? v.toISOString() : v,
z.string().min(1)) applied to the IsoTimestamp primitive. Centralized,
no publisher changes, works identically server + web (the parity test
still passes).

## Codecontext .codecontextignore auto-install

services/codecontext_client.ts now copies the
codecontext/.codecontextignore.template into any project's root on the
first call to that project if no .codecontextignore exists. One file
written per project, idempotent (in-memory Set guard + access-check),
silent fallback on read-only project. Stops the upstream empty-source-
file parser crash on foreign projects' node_modules — previously
required manually copying the template per project.

## Tool-call budget cap 30 → 50

services/inference/budget.ts: BUDGET_READ_ONLY and BUDGET_NO_AGENT
bumped to 50 (from 30). BUDGET_NON_READ_ONLY stays at 10 (no write
tools landed yet). Real recon sessions were hitting 30 with ~3 turns
wasted on codecontext parse failures; legitimate need was ~27, and
Architect-class system overviews want deeper recon. Headroom of 20
absorbs failure-retry turns without changing the safety floor — the
doom-loop guard (3 identical calls → abort) catches the actual
failure mode this cap was guarding against.

v1.14 (Phase C outer agent loop) will supersede this via per-agent
agent.steps. Throwaway-ish patch but unblocks deeper recon today.

## UI cleanups

- ChatPane queued-message dropdown removed. Each queued message now
  has three buttons: edit (pop back into ChatInput via sendToChat
  event), force-send (was the dropdown's only useful action), and
  cancel. Default behavior (send when streaming completes) needs no
  UI — it's the implicit do-nothing path.
- ChatThroughput removed from desktop tab strip (ChatTabBar.tsx).
  Mobile tab switcher still shows it.

## Plumbing

- .gitignore: data/* + !data/AGENTS.md + !data/skills/ negation
  patterns so the vendored skill library + agent registry become
  git-tracked while session DB state stays out.
- docker-compose.yml: removed /opt/skills:/data/skills override
  mount. Skills now live in the boocode repo at data/skills/,
  auditable per-batch. The host-level /opt/skills/ is preserved
  untouched for any other tools that read from it.
- .codecontextignore at repo root: auto-installed when codecontext
  was first called against /opt/boocode itself; matches the template.
- CLAUDE.md: updated to document the v1.13.11 publishFrame wrapper +
  message_parts table + tool_cost_stats view + DB-integration test
  pattern + host-side smoke endpoint quirk. (Pre-existing in working
  tree before this batch; shipped here for completeness.)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

apps/server/src/services/codecontext_client.ts

@@ -16,9 +16,41 @@
 //      file parser bug (upstream issue #37) returns a generic error string,
 //      which we re-surface with a hint to add the file to .codecontextignore.
 
-import { realpath } from 'node:fs/promises';
+import { access, copyFile, realpath } from 'node:fs/promises';
+import { join } from 'node:path';
 import { truncateIfNeeded } from './truncate.js';
 
+// v1.13.12 fix: codecontext crashes on empty source files (upstream issue #37)
+// when it can't ignore them. The .codecontextignore.template ships with the
+// project at /opt/boocode/codecontext/.codecontextignore.template (path inside
+// the container; the host's /opt is bind-mounted). On the first call to any
+// project, copy the template in if no per-project ignore exists yet. The user
+// can subsequently edit the file to customize. Idempotent — once any file is
+// at the project root we never overwrite.
+const IGNORE_TEMPLATE_PATH = '/opt/boocode/codecontext/.codecontextignore.template';
+const ensuredIgnoreProjects = new Set<string>();
+
+async function ensureIgnoreFile(projectRoot: string): Promise<void> {
+  if (ensuredIgnoreProjects.has(projectRoot)) return;
+  const ignorePath = join(projectRoot, '.codecontextignore');
+  try {
+    await access(ignorePath);
+    ensuredIgnoreProjects.add(projectRoot);
+    return;
+  } catch {
+    // missing — install the default
+  }
+  try {
+    await copyFile(IGNORE_TEMPLATE_PATH, ignorePath);
+    ensuredIgnoreProjects.add(projectRoot);
+  } catch {
+    // Template missing or project root read-only — proceed without it. The
+    // codecontext call may still crash on empty source files; the model gets
+    // the existing hint-message via the catch below telling it to add to
+    // .codecontextignore manually.
+  }
+}
+
 export interface CodecontextRequest {
   toolName: string;
   args: Record<string, unknown>;
@@ -46,6 +78,10 @@ export async function callCodecontext(
   // never pass target_dir; tests can override). A non-existent target_dir
   // throws before we hit the network so the model gets a sharp error.
   const resolvedProject = await realpath(req.projectPath);
+  // v1.13.12 fix: install the default .codecontextignore on first call to any
+  // project so codecontext doesn't crash on empty node_modules files. One file
+  // written per project, idempotent (set-membership check inside).
+  await ensureIgnoreFile(resolvedProject);
   const requestedTarget = req.args['target_dir'];
   const targetDir = typeof requestedTarget === 'string' && requestedTarget.length > 0
     ? requestedTarget

apps/server/src/services/inference/budget.ts

@@ -3,17 +3,24 @@ import { READ_ONLY_TOOL_NAMES } from '../tools.js';
 
 // v1.8.2: tool-call budget defaults. Resolved per-turn by resolveToolBudget.
 //   - Agent with explicit max_tool_calls: that value.
-//   - Agent with read-only-only tools:    BUDGET_READ_ONLY (30).
+//   - Agent with read-only-only tools:    BUDGET_READ_ONLY (50).
 //   - Agent with any non-read-only tool:  BUDGET_NON_READ_ONLY (10).
-//   - No agent (raw chat):                BUDGET_NO_AGENT (30).
+//   - No agent (raw chat):                BUDGET_NO_AGENT (50).
 // v1.13.7: bumped BUDGET_NO_AGENT 15→30 to match BUDGET_READ_ONLY. Every tool
 // in ALL_TOOLS today is read-only (see services/tools.ts comment at
 // READ_ONLY_TOOL_NAMES); the cautious 15-cap was a forward-looking guard for
 // write tools that haven't landed yet. No-agent mode gets the same toolset as
 // an all-read-only agent at runtime, so they should share the same budget.
-export const BUDGET_READ_ONLY = 30;
+// v1.13.12: bumped read-only caps 30→50. Real recon sessions were hitting 30
+// with ~3 turns wasted on codecontext parse failures (empty node_modules
+// files); legitimate need was ~27, and Architect-class system overviews want
+// deeper recon than a 30-cap permits. Headroom of 20 absorbs failure-retry
+// turns + deeper exploration without changing the safety floor materially —
+// the doom-loop guard (3 identical calls → abort) catches the actual failure
+// mode this cap was guarding against.
+export const BUDGET_READ_ONLY = 50;
 export const BUDGET_NON_READ_ONLY = 10;
-export const BUDGET_NO_AGENT = 30;
+export const BUDGET_NO_AGENT = 50;
 
 const READ_ONLY_SET: ReadonlySet<string> = new Set(READ_ONLY_TOOL_NAMES);
 

apps/server/src/types/ws-frames.ts

@@ -19,7 +19,17 @@ import { z } from 'zod';
 const Uuid = z.string().uuid();
 // Tool call IDs are model-emitted (e.g. "call_abc123") — not UUIDs.
 const ToolCallId = z.string().min(1);
-const IsoTimestamp = z.string().min(1);
+// v1.13.12 fix: postgres returns timestamp columns as JS Date objects, not
+// strings. The publish sites pass them through unchanged, so the schema must
+// tolerate both. preprocess converts Date → ISO string before string-validation;
+// on the web side (where frames arrive via JSON.parse) it's a no-op. Before
+// this fix, every message_complete / session_updated / chat_updated frame
+// failed validation and got dropped — symptoms: token tracking blank in UI,
+// status stuck at 'streaming' tripping the 60s stale-stream banner.
+const IsoTimestamp = z.preprocess(
+  (v) => (v instanceof Date ? v.toISOString() : v),
+  z.string().min(1),
+);
 
 const ChatStatusValue = z.enum([
   'streaming',