fix: resolve issues #543, #544, #545, #557 (#558)

* docs: add investigation reports for 5 open GitHub issues

Comprehensive analysis of issues #543, #544, #545, #555, and #557:

- #557: settings.json not generated, module loader error (node/bun mismatch)
- #555: Windows hooks not executing, hasIpc always false
- #545: formatTool crashes on non-JSON tool_input strings
- #544: mem-search skill hint shown incorrectly to Claude Code users
- #543: /claude-mem slash command unavailable despite installation

Each report includes root cause analysis, affected files, and proposed fixes.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(logger): handle non-JSON tool_input in formatTool (#545)

Wrap JSON.parse in try-catch to handle raw string inputs (e.g., Bash
commands) that aren't valid JSON. Falls back to using the string as-is.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(context): update mem-search hint to reference MCP tools (#544)

Update hint messages to reference MCP tools (search, get_observations)
instead of the deprecated "mem-search skill" terminology.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(settings): auto-create settings.json on first load (#557, #543)

When settings.json doesn't exist, create it with defaults instead of
returning in-memory defaults. Creates parent directory if needed.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(hooks): use bun runtime for hooks except smart-install (#557)

Change hook commands from node to bun since hooks use bun:sqlite.
Keep smart-install.js on node since it bootstraps bun installation.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* chore: rebuild plugin scripts

* docs: clarify that build artifacts must be committed

* fix(docs): update build artifacts directory reference in CLAUDE.md

* test: add test coverage for PR #558 fixes

- Fix 2 failing tests: update "mem-search skill" → "MCP tools" expectations
- Add 56 tests for formatTool() JSON.parse crash fix (Issue #545)
- Add 27 tests for settings.json auto-creation (Issue #543)

Test coverage includes:
- formatTool: JSON parsing, raw strings, objects, null/undefined, all tool types
- Settings: file creation, directory creation, schema migration, edge cases

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(tests): clean up flaky tests and fix circular dependency

Phase 1 of test quality improvements:

- Delete 6 harmful/worthless test files that used problematic mock.module()
  patterns or tested implementation details rather than behavior:
  - context-builder.test.ts (tested internal implementation)
  - export-types.test.ts (fragile mock patterns)
  - smart-install.test.ts (shell script testing antipattern)
  - session_id_refactor.test.ts (outdated, tested refactoring itself)
  - validate_sql_update.test.ts (one-time migration validation)
  - observation-broadcaster.test.ts (excessive mocking)

- Fix circular dependency between logger.ts and SettingsDefaultsManager.ts
  by using late binding pattern - logger now lazily loads settings

- Refactor mock.module() to spyOn() in several test files for more
  maintainable and less brittle tests:
  - observation-compiler.test.ts
  - gemini_agent.test.ts
  - error-handler.test.ts
  - server.test.ts
  - response-processor.test.ts

All 649 tests pass.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor(tests): phase 2 - reduce mock-heavy tests and improve focus

- Remove mock-heavy query tests from observation-compiler.test.ts, keep real buildTimeline tests
- Convert session_id_usage_validation.test.ts from 477 to 178 lines of focused smoke tests
- Remove tests for language built-ins from worker-spawn.test.ts (JSON.parse, array indexing)
- Rename logger-coverage.test.ts to logger-usage-standards.test.ts for clarity

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* docs(tests): phase 3 - add JSDoc mock justification to test files

Document mock usage rationale in 5 test files to improve maintainability:
- error-handler.test.ts: Express req/res mocks, logger spies (~11%)
- fallback-error-handler.test.ts: Zero mocks, pure function tests
- session-cleanup-helper.test.ts: Session fixtures, worker mocks (~19%)
- hook-constants.test.ts: process.platform mock for Windows tests (~12%)
- session_store.test.ts: Zero mocks, real SQLite :memory: database

Part of ongoing effort to document mock justifications per TESTING.md guidelines.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* test(integration): phase 5 - add 72 tests for critical coverage gaps

Add comprehensive test coverage for previously untested areas:

- tests/integration/hook-execution-e2e.test.ts (10 tests)
  Tests lifecycle hooks execution flow and context propagation

- tests/integration/worker-api-endpoints.test.ts (19 tests)
  Tests all worker service HTTP endpoints without heavy mocking

- tests/integration/chroma-vector-sync.test.ts (16 tests)
  Tests vector embedding synchronization with ChromaDB

- tests/utils/tag-stripping.test.ts (27 tests)
  Tests privacy tag stripping utilities for both <private> and
  <meta-observation> tags

All tests use real implementations where feasible, following the
project's testing philosophy of preferring integration-style tests
over unit tests with extensive mocking.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* context update

* docs: add comment linking DEFAULT_DATA_DIR locations

Added NOTE comment in logger.ts pointing to the canonical DEFAULT_DATA_DIR
in SettingsDefaultsManager.ts. This addresses PR reviewer feedback about
the fragility of having the default defined in two places to avoid
circular dependencies.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

src/shared/SettingsDefaultsManager.ts

@@ -5,11 +5,12 @@
  * Provides methods to get defaults with optional environment variable overrides.
  */
 
-import { readFileSync, writeFileSync, existsSync } from 'fs';
-import { join } from 'path';
+import { readFileSync, writeFileSync, existsSync, mkdirSync } from 'fs';
+import { join, dirname } from 'path';
 import { homedir } from 'os';
 import { DEFAULT_OBSERVATION_TYPES_STRING, DEFAULT_OBSERVATION_CONCEPTS_STRING } from '../constants/observation-metadata.js';
-import { logger } from '../utils/logger.js';
+// NOTE: Do NOT import logger here - it creates a circular dependency
+// logger.ts depends on SettingsDefaultsManager for its initialization
 
 export interface SettingsDefaults {
   CLAUDE_MEM_MODEL: string;
@@ -133,7 +134,19 @@ export class SettingsDefaultsManager {
   static loadFromFile(settingsPath: string): SettingsDefaults {
     try {
       if (!existsSync(settingsPath)) {
-        return this.getAllDefaults();
+        const defaults = this.getAllDefaults();
+        try {
+          const dir = dirname(settingsPath);
+          if (!existsSync(dir)) {
+            mkdirSync(dir, { recursive: true });
+          }
+          writeFileSync(settingsPath, JSON.stringify(defaults, null, 2), 'utf-8');
+          // Use console instead of logger to avoid circular dependency
+          console.log('[SETTINGS] Created settings file with defaults:', settingsPath);
+        } catch (error) {
+          console.warn('[SETTINGS] Failed to create settings file, using in-memory defaults:', settingsPath, error);
+        }
+        return defaults;
       }
 
       const settingsData = readFileSync(settingsPath, 'utf-8');
@@ -148,9 +161,9 @@ export class SettingsDefaultsManager {
         // Auto-migrate the file to flat schema
         try {
           writeFileSync(settingsPath, JSON.stringify(flatSettings, null, 2), 'utf-8');
-          logger.info('SETTINGS', 'Migrated settings file from nested to flat schema', { settingsPath });
+          console.log('[SETTINGS] Migrated settings file from nested to flat schema:', settingsPath);
         } catch (error) {
-          logger.warn('SETTINGS', 'Failed to auto-migrate settings file', { settingsPath }, error);
+          console.warn('[SETTINGS] Failed to auto-migrate settings file:', settingsPath, error);
           // Continue with in-memory migration even if write fails
         }
       }
@@ -165,7 +178,7 @@ export class SettingsDefaultsManager {
 
       return result;
     } catch (error) {
-      logger.warn('SETTINGS', 'Failed to load settings, using defaults', { settingsPath }, error);
+      console.warn('[SETTINGS] Failed to load settings, using defaults:', settingsPath, error);
       return this.getAllDefaults();
     }
   }