fix(mcp): add --tools CLI flag for CODEGRAPH_MCP_TOOLS fallback (#1192)

[umi008]

Summary

Adds codegraph serve --mcp --tools=<list> as a CLI fallback for the
CODEGRAPH_MCP_TOOLS env var. Some MCP clients (OpenCode, Antigravity
IDE) don't forward the env block from the MCP server config to the
spawned process, so users pinning the tool surface via
env.CODEGRAPH_MCP_TOOLS see only the default codegraph_explore
regardless of what they set.

Root cause

The filtering logic in getStaticTools() (proxy) and
ToolHandler.getTools() (direct / daemon) is correct — both read
process.env.CODEGRAPH_MCP_TOOLS at call time. The bug is that some
MCP clients don't inject the env block from the MCP config into the
spawned process, so process.env.CODEGRAPH_MCP_TOOLS is empty when
the server reads it.

Fix

Add a --tools flag to the serve --mcp command. The flag is parsed
by commander and sets process.env.CODEGRAPH_MCP_TOOLS before
MCPServer construction, so it propagates through every runtime path:

1. Proxy — runLocalHandshakeProxy → getStaticTools() reads the
   env var at call time.
2. Daemon — the spawn uses env: { ...process.env } (line 156 in
   src/mcp/index.ts), so the daemon inherits the env var from the
   launcher.
3. Direct mode — ToolHandler.getTools() → toolAllowlist()
   reads the env var.

The CLI flag wins over a pre-set env var so the operator's explicit
intent in the MCP config is always honored. An empty value is treated as
unset to match the existing whitespace-only env-var behavior in
toolAllowlist().

Validation

• New test suite __tests__/cli-mcp-tools-flag.test.ts exercises
  end-to-end against the built binary:
  • default surface (only codegraph_explore) when --tools is omitted
  • requested surface when --tools=explore,search,node
  • single-tool allowlist (--tools=callers)
  • empty value falls back to the default
  • --tools wins when both flag and env var are set
  • the proxy path also honors --tools (env var set in the
    launcher process before the proxy intercepts tools/list)
• All 6 new tests pass on Linux + macOS.
• Existing mcp-tool-allowlist.test.ts (7 tests) and
  mcp-initialize.test.ts (3 tests) still pass — no regression.

Reproduction

// .mcp.json (works on Claude Code, Cursor, Codex CLI, Kiro)
{
  "mcpServers": {
    "codegraph": {
      "command": "codegraph",
      "env": { "CODEGRAPH_MCP_TOOLS": "explore,search,node" }
    }
  }
}

// .mcp.json (works on opencode, Antigravity IDE — the env block is ignored)
{
  "mcpServers": {
    "codegraph": {
      "command": "codegraph",
      "args": ["serve", "--mcp", "--tools=explore,search,node"]
    }
  }
}

Closes #1192