[codex] improve graph CLI for large repos

[jayhack]

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 Git config writes for read-only graph inspection.
• Add a site-native /cli reference page for the new high-level agent command surface, avoiding the retired Mintlify docs path.

Impact

• Full ClickUp sd TypeScript repo parsing works with the Rust backend: 12,045 files in ~14-15s locally.
• sd parse memory is about 0.6 GB peak RSS: built-in diagnose reported 615.9 MB peak RSS; /usr/bin/time -l reported 608,649,216 bytes max RSS.
• Full-repo symbols, inspect, and outbound callgraph work against sd with --backend rust --fallback error.
• Rust compact inbound callgraph returns 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 --frozen pre-commit run --show-diff-on-failure --color=always --all-files --source origin/develop --origin HEAD
• 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 ty check --output-format=concise src/graph_sitter/git/repo_operator/repo_operator.py src/graph_sitter/typescript/config_parser.py src/graph_sitter/typescript/ts_config.py src/graph_sitter/cli/commands/callgraph/main.py src/graph_sitter/cli/commands/symbols/main.py src/graph_sitter/cli/cli.py src/graph_sitter/cli/commands/graph/common.py src/graph_sitter/cli/commands/rename/main.py src/graph_sitter/cli/commands/usages/main.py src/graph_sitter/cli/commands/using/main.py
• uv run pytest 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
• rust-rewrite/tools/check_fast.sh
• 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 diagnose /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --json
• /usr/bin/time -l 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 --max-results 5 --format json
• uv run graph-sitter inspect packages/ai-agent-harness/src/inference.ts /Users/jayhack/CS/CLICKUP/sd --language typescript --backend rust --fallback error --level functions --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 1 --max-results 12 --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 --max-results 12 --format json
• Parallel sd smoke: symbols, outbound callgraph, and inbound callgraph ran together without Git config lock errors; /Users/jayhack/CS/CLICKUP/sd stayed clean.

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Project	Deployment	Actions	Updated (UTC)
graph-sitter	Ready	Preview, Comment	Jun 24, 2026 3:05am

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Project	Status	Preview	Updated (UTC)
graph-sitter	🔴 Failed	–	Jun 24, 2026, 2:48 AM

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