feat(tools): support per-tool timeout override for council runs

docs/plans/state.json

@@ -3,6 +3,21 @@
   "updated_at": "2026-02-23",
   "description": "Tracks the status of all Flynn plans and implementation phases",
   "plans": {
+    "council-tool-timeout-override": {
+      "status": "completed",
+      "date": "2026-02-23",
+      "updated": "2026-02-23",
+      "summary": "Added optional per-tool timeout override support in ToolExecutor and set `council.run` to 180000ms so council orchestration in the native tool loop is no longer hard-capped by the global 30000ms tool timeout.",
+      "files_modified": [
+        "src/tools/types.ts",
+        "src/tools/executor.ts",
+        "src/tools/executor.test.ts",
+        "src/tools/builtin/council-run.ts",
+        "src/tools/builtin/council-run.test.ts",
+        "docs/plans/state.json"
+      ],
+      "test_status": "pnpm test:run src/tools/executor.test.ts src/tools/builtin/council-run.test.ts + pnpm typecheck passing"
+    },
     "gmail-filter-scope-correction": {
       "status": "completed",
       "date": "2026-02-23",
@@ -6340,7 +6355,7 @@
     }
   },
   "overall_progress": {
-    "total_test_count": 1965,
+    "total_test_count": 1967,
     "all_tests_passing": true,
     "p0_completion": "3/3 (100%)",
     "p1_completion": "4/4 (100%)",
@@ -6362,6 +6377,7 @@
     "gmail_filter_creation": "completed — gmail.filter.create tool added with criteria/action validation; gmail-auth requests explicit gmail.settings.basic + gmail.readonly scopes for filter creation and inbox reads",
     "toolloop_action_intent_recovery": "completed — when a model claims it will execute a tool but emits no tool call, NativeAgent now issues one internal nudge and continues the same turn to execute tools or produce a concrete blocker",
     "toolloop_execution_claim_recovery": "completed — when a model claims a known tool already succeeded/failed without emitting a tool call, NativeAgent now nudges once and retries the same turn before returning text",
+    "council_tool_timeout_override": "completed — ToolExecutor supports per-tool timeout overrides and council.run now uses a 180s timeout to avoid false 30s council timeouts in the tool loop",
     "minimal_tui_multiline_paste_mode": "completed — minimal TUI now supports `/paste`/`/multiline` multiline compose mode ending with single '.' line, preventing newline truncation for pasted prompts",
     "native_audio_support": "completed — smart routing for native audio (Gemini/OpenAI/GitHub) vs Whisper transcription fallback, plus 2026-02-23 arg hydration hardening, tool.args_rewritten audit metric, transient fetch retry/timeout hardening, localhost->127.0.0.1 fallback for transcription endpoint connectivity, and whisper docker-compose entrypoint arg fix for port 18801",
     "remaining_phases_completion": "Phase 1: 3/3 (100%) — context levels, command registry, memory structure. Phase 2: 3/3 (100%) — component registry, confidence routing, history index. Phase 3: 2/2 (100%) — adaptive memory/compaction, truthfulness/autonomy hardening",