MCP-T13 + T14: cgraph init-agent + Docker dual-mode

[DvirDukhan]

MCP-T13 + T14 — agent guidance bundle & Docker dual-mode

Stacked on #682 (T12 auto-init). Closes #661 and #662.

T13 — cgraph init-agent

Two canonical guidance files now ship as package data under
api/mcp/templates/:

• claude_mcp_section.md — full 8-tool table + rules of thumb
  (start with search_code; prefer structural tools over ask;
  run impact_analysis before refactoring).
• cursorrules.template — Cursor-flavoured tool-selection rules.

New Typer command drops them into the current directory:

cgraph init-agent          # refuses to overwrite
cgraph init-agent --force  # clobber

AGENTS.md updated with the MCP section pointing at this command and
the supported env vars (CODE_GRAPH_AUTO_INDEX, CGRAPH_MODE).

T14 — Dockerised dual-mode

Same image now runs either the FastAPI web app or the MCP stdio
server based on CGRAPH_MODE:

# web (default, unchanged behaviour)
docker compose up code-graph

# mcp stdio
docker compose --profile mcp run --rm -i code-graph-mcp

start.sh dispatches on CGRAPH_MODE=web|mcp. docker-compose.yml
gains an opt-in code-graph-mcp service guarded by the mcp
profile (no impact on the default up). README quickstart covers
both claude mcp add-json and the Docker path.

Tests

• 4 new CliRunner tests in tests/mcp/test_init_agent.py (write,
  refuse-overwrite, force-overwrite, package-data sanity).
• Full MCP suite green: 61 passed in 23.3s locally.
• bash -n start.sh clean.

Followups

• T18 (incremental indexing, MCP T18 — Incremental indexing (file-hash based) #665) is the only Phase-1 ticket left;
  non-trivial and out of scope for this PR.

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