feat(mcp): add codebase exploration tools

[ethansara92-beep]

Closes #309

Summary

• add MCP grep, status, and codebase_overview tools
• add persistent source-tree freshness tracking and return freshness.stale / freshness.indexed_at from MCP search and status responses
• surface freshness in ccc status and remove its derived state with ccc reset

Motivation

MCP previously exposed only semantic search. Agents could not use ccc's AST-based structural search, inspect index state, or cheaply orient in an unfamiliar repository. They also had no signal that a non-refreshed semantic search could be using an outdated index.

Implementation notes

• Freshness fingerprints indexable paths, mtimes, sizes, and project settings after every successful index update.
• The fingerprint and index timestamp are stored in the derived index_state.json, so they survive daemon restarts.
• A source or settings mismatch, an indexing run in progress, an index error, or missing legacy state reports stale: true.
• Structural grep is constrained to paths inside the configured project and returns exact matched spans with line ranges.

Validation

• uv run prek run --all-files
• uv run pytest tests/ -q
• uv run mypy .