Implement database migration framework and performance optimizations

- Added active memory configuration for manual interval and Gemini tool.
- Created file modification rules for handling edits and writes.
- Implemented migration manager for managing database schema migrations.
- Added migration 001 to normalize keywords into separate tables.
- Developed tests for validating performance optimizations including keyword normalization, path lookup, and symbol search.
- Created validation script to manually verify optimization implementations.

.claude/rules/file-modification.md

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+## File Modification
+
+### Use edit_file (MCP)
+- Built-in Edit tool failed 1+ times
+- Need dry-run preview before applying changes
+- Need line-based operations (insert_after, insert_before)
+- Need to replace all occurrences at once
+- Built-in Edit returns "old_string not found"
+- Whitespace/formatting issues in built-in Edit
+
+**Mode Selection**:
+- `mode=update`: Replace text
+- `mode=line`: Line-based operations
+
+### Use write_file (MCP)
+- Creating brand new files
+- MCP edit_file still fails (last resort)
+- Need to completely replace file content
+- Need backup before overwriting
+- User explicitly asks to "recreate file"
+
+## Priority Logic
+
+**File Reading**:
+1. Known single file → Built-in Read
+2. Multiple files OR pattern matching → read_file (MCP)
+3. Unknown location → smart_search then Read
+4. Large codebase + repeated access → codex_lens
+
+**File Editing**:
+1. Always try built-in Edit first
+2. Fails 1+ times → edit_file (MCP)
+3. Still fails → write_file (MCP)
+
+**Search**:
+1. External knowledge → Exa
+2. Exact pattern in small codebase → Built-in Grep
+3. Semantic/unknown location → smart_search
+4. Large codebase + repeated searches → codex_lens
+
+## Decision Triggers
+
+**Start with simplest tool** (Read, Edit, Grep)
+**Escalate to MCP tools** when built-ins fail or inappropriate
+**Use semantic search** for exploratory tasks
+**Use indexed search** for large, stable codebases
+**Use Exa** for external/public knowledge