fix: automatic recognition of root

[isink17]

What

Makes --repo-root optional across all CLI commands and MCP tools.

Why

Users had to hardcode absolute paths in editor configs, causing setup
failures (especially on Windows where Claude Code doesn't inherit PATH).

How

Added config.ResolveRepoRoot() with 5-step fallback:

1. explicit --repo-root flag
2. per-call MCP tool parameter
3. git rev-parse --show-toplevel
4. os.Getwd()
5. error

All CLI commands and MCP tools route through this helper.

[gemini-code-assist]

Code Review

This pull request implements automatic repository root detection for the codegraph tool, making the --repo-root flag optional across various commands and the MCP server. The resolution logic follows a fallback chain including explicit flags, tool parameters, git root detection, and the current working directory. Review feedback identifies a priority issue in the ResolveRepoRoot function where the global CLI flag currently takes precedence over the more specific MCP tool parameter; it is recommended to swap these to ensure local overrides are respected. Corresponding updates to the test suite are also suggested to verify this corrected behavior.