[codex] add graph query CLI commands

[jayhack]

Summary

• Add high-level graph CLI commands: inspect, using, usages, and rename.
• Add target resolution for FILE:SYMBOL, FILE::SYMBOL, and dotted file shorthand.
• Add CLI reference docs and uvx examples for graph queries and focused renames.

Impact

• Agents and automation can inspect file structure, trace inbound/outbound call graphs, and perform resolved renames without writing one-off codemods.
• rename defaults to dry-run behavior and requires --write to modify files.
• The PR branch is rebased on current develop, which already contains the Agent/API removal from Remove Agent and AI APIs #165.

Validation

• uv run ruff check src/graph_sitter/cli/cli.py src/graph_sitter/cli/commands/graph/common.py src/graph_sitter/cli/commands/inspect/main.py src/graph_sitter/cli/commands/using/main.py src/graph_sitter/cli/commands/usages/main.py src/graph_sitter/cli/commands/rename/main.py tests/unit/cli/commands/graph/test_graph_commands.py
• uv run pytest tests/unit/cli/commands/parse/test_parse.py tests/unit/cli/commands/run/test_run.py tests/unit/cli/commands/graph/test_graph_commands.py
• PATH="$HOME/.nvm/versions/node/v22.19.0/bin:$PATH" npm --prefix site run build

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1 Skipped Deployment

Project	Deployment	Actions	Updated (UTC)
graph-sitter	Ignored	Preview	Jun 23, 2026 7:09pm