feat: implement full spy-code codebase — replace all stubs with working code

[Copilot]

The project was at ~M3 with all crates beyond spy-core/spy-storage/spy-resolvers(Rust-only) either stubbed or missing key functionality. This PR completes M4–M9: multi-language parsing, git integration, full GraphQL/MCP wiring, and incremental indexing.

spy-git

Full git integration via std::process::Command (no gix — feature-flag hell). Implements GitRepo::discover(), current_sha(), is_dirty(), diff_files_since(), files_changed_since_ref().

spy-parser + spy-resolvers

Extends Rust-only parser to Python, TypeScript, JavaScript, Go by upgrading tree-sitter 0.24→0.26 and adding grammar crates. Each language gets a resolver extracting:

• Functions/methods with typed signatures
• Classes/structs/interfaces
• Module-level constants
• Call edges (BFS-resolved against ProjectScope)
• Doc comments / docstrings / JSDoc

Special handling: @overload collapse for Python/TypeScript merges overload variants into a single node with multiple signatures.

spy-storage

Added list_files() and get_nodes_for_files(file_paths) — both needed by graph and MCP layers.

spy-graph

• files query: now queries DB instead of returning []
• changedSince(ref): shells to git diff --name-only, maps changed paths to indexed nodes
• callers/callees: upgraded from single-hop to multi-hop BFS via depth param

spy-indexer

• Multi-language file discovery (.rs/.py/.ts/.tsx/.js/.go) with configurable ignore dirs
• Two-pass indexing: pass 1 extracts nodes (builds ProjectScope), pass 2 extracts edges using full scope — necessary because call resolution requires the complete node set
• Git-based incremental mode: git diff <last_sha>..HEAD --name-status → parse only changed/added files, delete nodes for removed files, handle renames
• Content-hash fallback when outside a git repo

spy-mcp

Full stdio JSON-RPC 2.0 MCP server. Seven tools: query_graph, get_node, search, find_callers, find_callees, changed_since, stats. Three resources: spy-code://schema, spy-code://stats, spy-code://config.

spy-cli

Wired cmd_changed (git diff → node list) and cmd_serve --mcp → spy_mcp::run_mcp_server. Fixed depth arg passthrough in callers/callees.

Tests

6 integration tests in spy-indexer/tests/integration.rs covering all 4 language fixture sets plus an incremental-skip test. Fixture files added under tests/fixtures/{rust,python,ts,go}_sample/.