Summary

• Add agent-friendly graph CLI commands: symbols for target discovery and callgraph for clean local call graph traversal.
• Improve existing graph commands with --resolved-only, --local-only, --hide-runtime, and --dedupe filters, plus affected-file reporting in rename --check.
• Fix large TypeScript monorepo parsing by resolving directory project references to tsconfig.json and avoiding unnecessary git init on existing repos.
• Update CLI docs and uvx workflows for full-repo Rust-backed discovery and scoped Python callgraph workflows.

Impact

• Full ClickUp sd TypeScript repo parsing works with the Rust backend: 12,045 files in ~15s locally.
• Full-repo symbols, inspect, and outbound callgraph work against sd with --backend rust --fallback error.
• Rust compact inbound callgraph now falls back to file-level usage edges; scoped Python still provides function-level inbound caller recursion.
• Existing using, usages, and rename behavior remains available, with new filters for cleaner agent output.

Validation

• uv run ruff check src/graph_sitter/typescript/config_parser.py src/graph_sitter/typescript/ts_config.py src/graph_sitter/git/repo_operator/repo_operator.py src/graph_sitter/cli/cli.py src/graph_sitter/cli/commands/graph/common.py src/graph_sitter/cli/commands/using/main.py src/graph_sitter/cli/commands/usages/main.py src/graph_sitter/cli/commands/callgraph/main.py src/graph_sitter/cli/commands/symbols/main.py src/graph_sitter/cli/commands/rename/main.py tests/unit/cli/commands/graph/test_graph_commands.py tests/unit/cli/commands/parse/test_parse.py
• uv run pytest tests/unit/cli/commands/graph/test_graph_commands.py tests/unit/cli/commands/parse/test_parse.py tests/unit/cli/commands/run/test_run.py tests/unit/cli/commands/transform/test_transform.py
• PATH="$HOME/.nvm/versions/node/v22.19.0/bin:$PATH" npm --prefix site run build
• uv run graph-sitter parse /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --format json
• uv run graph-sitter symbols runInference /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --kind function --format json
• uv run graph-sitter callgraph packages/ai-agent-harness/src/inference.ts.runInference /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --depth 2 --format json
• uv run graph-sitter callgraph packages/ai-agent-harness/src/inference.ts.runInference /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --direction inbound --depth 1 --format json
• uv run graph-sitter parse /Users/jayhack/CS/CLICKUP/sd --language typescript --backend python --subdir packages/ai-agent-harness/src --format json