chore: clean up development artifacts and update .gitignore

- Remove AI agent coordination files and progress tracking
- Remove temporary test results and generated artifacts
- Remove diagnostic test scripts from src/scripts/
- Remove development planning documents
- Update .gitignore to exclude test artifacts
- Clean up 53 temporary files total

tests/integration/database/TRANSACTION_TEST_FIXES.md

@@ -1,38 +0,0 @@
-# Transaction Test Fixes Summary
-
-## Fixed Issues
-
-### 1. Updated SQL Statements to Match Schema
-- Changed all INSERT statements to use the correct column names:
-  - `name` → `node_type` (PRIMARY KEY)
-  - `type` → removed (not in schema)
-  - `package` → `package_name`
-  - Added all required columns: `description`, `category`, `development_style`, `is_ai_tool`, `is_trigger`, `is_webhook`, `is_versioned`, `documentation`, `properties_schema`, `operations`, `credentials_required`
-
-### 2. Fixed Parameter Count Mismatches
-- Updated all `.run()` calls to have 15 parameters matching the 15 placeholders in INSERT statements
-- Added proper data transformations:
-  - Boolean fields converted to 0/1 (e.g., `node.isAITool ? 1 : 0`)
-  - JSON fields stringified (e.g., `JSON.stringify(node.properties || [])`)
-
-### 3. Fixed Object Property References
-- Changed all `node.name` references to `node.nodeType`
-- Updated all property accesses to match TestDataGenerator output
-
-### 4. Fixed Better-SQLite3 API Usage
-- Removed `.immediate()` and `.exclusive()` methods which don't exist in better-sqlite3
-- For exclusive transactions, used raw SQL: `BEGIN EXCLUSIVE`
-
-### 5. Adjusted Performance Test Expectations
-- Removed unrealistic performance expectations that were causing flaky tests
-- Changed to simply verify successful completion
-
-### 6. Fixed Constraint Violation Test
-- Updated to test PRIMARY KEY constraint on `node_type` instead of non-existent UNIQUE constraint on `name`
-- Updated error message expectation to match SQLite's actual error
-
-## Key Learnings
-1. Always verify the actual database schema before writing tests
-2. Count the number of placeholders vs parameters carefully
-3. Better-sqlite3 doesn't have all the transaction methods that might be expected
-4. Performance tests should be careful about making assumptions about execution speed