roam-code 9.0.0__tar.gz → 11.0.0__tar.gz

roam_code-11.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: roam-code
+Version: 11.0.0
+Summary: Instant codebase comprehension for AI coding agents
+Author: CosmoHac
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Cranot/roam-code
+Project-URL: Documentation, https://github.com/Cranot/roam-code#readme
+Project-URL: Repository, https://github.com/Cranot/roam-code
+Project-URL: Issues, https://github.com/Cranot/roam-code/issues
+Keywords: code-intelligence,static-analysis,mcp-server,tree-sitter,architecture,code-graph,ai-coding,graph-analysis,code-quality,cli,codebase,code-analysis,ai-tools,mcp
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Quality Assurance
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click>=8.0
+Requires-Dist: tree-sitter>=0.23
+Requires-Dist: tree-sitter-language-pack>=0.6
+Requires-Dist: networkx>=3.0
+Provides-Extra: mcp
+Requires-Dist: fastmcp>=2.0; extra == "mcp"
+Provides-Extra: semantic
+Requires-Dist: numpy>=1.24; extra == "semantic"
+Requires-Dist: onnxruntime>=1.16; extra == "semantic"
+Requires-Dist: tokenizers>=0.15; extra == "semantic"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.0; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+
+# roam-code
+
+**The architectural intelligence layer for AI coding agents. Structural graph, architecture governance, multi-agent orchestration, vulnerability mapping, runtime analysis -- one CLI, zero API keys.**
+
+*137 commands · 101 MCP tools · 26 languages · 100% local*
+
+[![PyPI version](https://img.shields.io/pypi/v/roam-code?style=flat-square&color=blue)](https://pypi.org/project/roam-code/)
+[![GitHub stars](https://img.shields.io/github/stars/Cranot/roam-code?style=flat-square)](https://github.com/Cranot/roam-code/stargazers)
+[![CI](https://github.com/Cranot/roam-code/actions/workflows/roam-ci.yml/badge.svg)](https://github.com/Cranot/roam-code/actions/workflows/roam-ci.yml)
+[![Python 3.9+](https://img.shields.io/badge/python-3.9+-3776AB?logo=python&logoColor=white)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+---
+
+## What is Roam?
+
+Roam is a structural intelligence engine for software. It pre-indexes your codebase into a semantic graph -- symbols, dependencies, call graphs, architecture layers, git history, and runtime traces -- stored in a local SQLite DB. Agents query it via CLI or MCP instead of repeatedly grepping files and guessing structure.
+
+Unlike LSPs (editor-bound, language-specific) or Sourcegraph (hosted search), Roam provides architecture-level graph queries -- offline, cross-language, and compact. It goes beyond comprehension: Roam governs architecture through budget gates, simulates refactoring outcomes, orchestrates multi-agent swarms with zero-conflict guarantees, maps vulnerability reachability paths, and enables graph-level code editing without syntax errors.
+
+```
+Codebase ──> [Index] ──> Semantic Graph ──> 137 Commands ──> AI Agent
+              │              │                  │
+           tree-sitter    symbols            comprehend
+           26 languages   + edges            govern
+           git history    + metrics          refactor
+           runtime traces + architecture     orchestrate
+```
+
+### The problem
+
+Coding agents explore codebases inefficiently: dozens of grep/read cycles, high token cost, no structural understanding. Roam replaces this with one graph query:
+
+```
+$ roam context Flask
+Callers: 47  Callees: 3
+Affected tests: 31
+
+Files to read:
+  src/flask/app.py:76-963              # definition
+  src/flask/__init__.py:1-15           # re-export
+  src/flask/testing.py:22-45           # caller: FlaskClient.__init__
+  tests/test_basic.py:12-30            # caller: test_app_factory
+  ...12 more files
+```
+
+### Terminal demo
+
+![roam terminal demo](docs/assets/roam-terminal-demo.gif)
+
+### Core commands
+
+```bash
+$ roam understand              # full codebase briefing
+$ roam context <name>          # files-to-read with exact line ranges
+$ roam preflight <name>        # blast radius + tests + complexity + architecture rules
+$ roam health                  # composite score (0-100)
+$ roam diff                    # blast radius of uncommitted changes
+```
+
+## What's New in v11
+
+### MCP v2 for Agent-First Workflows
+- In-process MCP execution removes per-call subprocess overhead.
+- 4 compound operations (`roam_explore`, `roam_prepare_change`, `roam_review_change`, `roam_diagnose_issue`) reduce multi-step agent workflows to single calls.
+- Preset-based tool surfacing (`core`, `review`, `refactor`, `debug`, `architecture`, `full`) keeps default tool choice tight for agents while retaining full depth on demand.
+- MCP tools now expose structured schemas and richer annotations for safer planner behavior.
+- MCP token overhead for default core context dropped from ~36K to <3K tokens (about 92% reduction).
+
+### Performance and Retrieval
+- Symbol search moved to SQLite FTS5/BM25: typical search moved from seconds to milliseconds (about 1000x on benchmarked paths).
+- Incremental indexing shifted from O(N) full-edge rebuild behavior to O(changed) updates.
+- DB/runtime optimizations (`mmap_size`, safer large-graph guards, batched writes) reduce first-run and reindex friction on larger repos.
+
+### CI, Governance, and Delivery
+- GitHub Action supports quality gates, SARIF upload, sticky PR comments, and cache-aware execution.
+- CI hardening includes changed-only analysis mode, trend-aware gates, and SARIF pre-upload guardrails (size/result caps + truncation signaling).
+- Agent governance expanded with verification and AI-quality tooling (`roam verify`, `roam vibe-check`, `roam ai-readiness`, `roam ai-ratio`) for teams managing agent-written code.
+
+## Best for
+
+- **Agent-assisted coding** -- structured answers that reduce token usage vs raw file exploration
+- **Large codebases (100+ files)** -- graph queries beat linear search at scale
+- **Architecture governance** -- health scores, CI quality gates, budget enforcement, fitness functions
+- **Safe refactoring** -- blast radius, affected tests, pre-change safety checks, graph-level editing
+- **Multi-agent orchestration** -- partition codebases for parallel agent work with zero-conflict guarantees
+- **Security analysis** -- vulnerability reachability mapping, auth gaps, CVE path tracing
+- **Algorithm optimization** -- detect O(n^2) loops, N+1 queries, and 21 other anti-patterns with suggested fixes
+- **Backend quality** -- auth gaps, missing indexes, over-fetching models, non-idempotent migrations, orphan routes, API drift
+- **Runtime analysis** -- overlay production trace data onto the static graph for hotspot detection
+- **Multi-repo projects** -- cross-repo API edge detection between frontend and backend
+
+### When NOT to use Roam
+
+- **Real-time type checking** -- use an LSP (pyright, gopls, tsserver). Roam is static and offline.
+- **Small scripts (<10 files)** -- just read the files directly.
+- **Pure text search** -- ripgrep is faster for raw string matching.
+
+## Why use Roam
+
+**Speed.** One command replaces 5-10 tool calls (in typical workflows). Under 0.5s for any query.
+
+**Dependency-aware.** Computes structure, not string matches. Knows `Flask` has 47 dependents and 31 affected tests. `grep` knows it appears 847 times.
+
+**LLM-optimized output.** Plain ASCII, compact abbreviations (`fn`, `cls`, `meth`), `--json` envelopes. Designed for agent consumption, not human decoration.
+
+**Fully local.** No API keys, telemetry, or network calls. Works in air-gapped environments.
+
+**Algorithm-aware.** Built-in catalog of 23 anti-patterns. Detects suboptimal algorithms (quadratic loops, N+1 queries, unbounded recursion) and suggests fixes with Big-O improvements and confidence scores. Receiver-aware loop-invariant analysis minimizes false positives.
+
+**CI-ready.** `--json` output, `--gate` quality gates, GitHub Action, SARIF 2.1.0.
+
+|  | Without Roam | With Roam |
+|--|-------------|-----------|
+| Tool calls | 8 | **1** |
+| Wall time | ~11s | **<0.5s** |
+| Tokens consumed | ~15,000 | **~3,000** |
+
+*Measured on a typical agent workflow in a 200-file Python project (Flask). See [benchmarks](#performance) for more.*
+
+<details>
+<summary><strong>Table of Contents</strong></summary>
+
+**Getting Started:** [What is Roam?](#what-is-roam) · [What's New in v11](#whats-new-in-v11) · [Best for](#best-for) · [Why use Roam](#why-use-roam) · [Install](#install) · [Quick Start](#quick-start)
+
+**Using Roam:** [Commands](#commands) · [Walkthrough](#walkthrough-investigating-a-codebase) · [AI Coding Tools](#integration-with-ai-coding-tools) · [MCP Server](#mcp-server)
+
+**Operations:** [CI/CD Integration](#cicd-integration) · [SARIF Output](#sarif-output) · [For Teams](#for-teams)
+
+**Reference:** [Language Support](#language-support) · [Performance](#performance) · [How It Works](#how-it-works) · [How Roam Compares](#how-roam-compares) · [FAQ](#faq)
+
+**More:** [Limitations](#limitations) · [Troubleshooting](#troubleshooting) · [Update / Uninstall](#update--uninstall) · [Development](#development) · [Contributing](#contributing)
+
+</details>
+
+## Install
+
+```bash
+pip install roam-code
+
+# Recommended: isolated environment
+pipx install roam-code
+# or
+uv tool install roam-code
+
+# From source
+pip install git+https://github.com/Cranot/roam-code.git
+```
+
+Requires Python 3.9+. Works on Linux, macOS, and Windows.
+
+> **Windows:** If `roam` is not found after installing with `uv`, run `uv tool update-shell` and restart your terminal.
+
+### Docker (alpine-based)
+
+```bash
+docker build -t roam-code .
+docker run --rm -v "$PWD:/workspace" roam-code index
+docker run --rm -v "$PWD:/workspace" roam-code health
+```
+
+## Quick Start
+
+```bash
+cd your-project
+roam init                  # indexes codebase, creates config + CI workflow
+roam understand            # full codebase briefing
+```
+
+First index takes ~5s for 200 files, ~15s for 1,000 files. Subsequent runs are incremental and near-instant.
+
+**Next steps:**
+
+- **Set up your AI agent:** `roam describe --write` (auto-detects CLAUDE.md, AGENTS.md, .cursor/rules, etc. — see [integration instructions](#integration-with-ai-coding-tools))
+- **Explore:** `roam health` → `roam weather` → `roam map`
+- **Add to CI:** `roam init` already generated a GitHub Action
+
+<details>
+<summary><strong>Try it on Roam itself</strong></summary>
+
+```bash
+git clone https://github.com/Cranot/roam-code.git
+cd roam-code
+pip install -e .
+roam init
+roam understand
+roam health
+```
+
+</details>
+
+## Works With
+
+<p align="center">
+  <a href="#integration-with-ai-coding-tools">Claude Code</a> &bull;
+  <a href="#integration-with-ai-coding-tools">Cursor</a> &bull;
+  <a href="#integration-with-ai-coding-tools">Windsurf</a> &bull;
+  <a href="#integration-with-ai-coding-tools">GitHub Copilot</a> &bull;
+  <a href="#integration-with-ai-coding-tools">Aider</a> &bull;
+  <a href="#integration-with-ai-coding-tools">Cline</a> &bull;
+  <a href="#integration-with-ai-coding-tools">Gemini CLI</a> &bull;
+  <a href="#integration-with-ai-coding-tools">OpenAI Codex CLI</a> &bull;
+  <a href="#mcp-server">MCP</a> &bull;
+  <a href="#cicd-integration">GitHub Actions</a> &bull;
+  <a href="#cicd-integration">GitLab CI</a> &bull;
+  <a href="#cicd-integration">Azure DevOps</a>
+</p>
+
+## Commands
+
+The [5 core commands](#core-commands) shown above cover ~80% of agent workflows. All 137 commands are organized into 7 categories.
+
+<details>
+<summary><strong>Full command reference</strong></summary>
+
+### Getting Started
+
+| Command | Description |
+|---------|-------------|
+| `roam index [--force] [--verbose]` | Build or rebuild the codebase index |
+| `roam watch [--interval N] [--debounce N] [--webhook-port P] [--guardian]` | Long-running index daemon: poll/webhook-triggered refreshes plus optional continuous architecture-guardian snapshots and JSONL compliance artifacts |
+| `roam init` | Guided onboarding: creates `.roam/fitness.yaml`, CI workflow, runs index, shows health |
+| `roam hooks [--install] [--uninstall]` | Manage git hooks for automated roam index updates and health gates |
+| `roam doctor` | Diagnose installation and environment: verify tree-sitter grammars, SQLite, git, and config health |
+| `roam reset [--hard]` | Reset the roam index and cached data. `--hard` removes all `.roam/` artifacts |
+| `roam clean [--all]` | Remove stale or orphaned index entries without a full rebuild |
+| `roam understand` | Full codebase briefing: tech stack, architecture, key abstractions, health, conventions, complexity overview, entry points |
+| `roam onboard` | Structured onboarding guide: architecture map, key files, suggested reading order, and first tasks |
+| `roam tour [--write PATH]` | Auto-generated onboarding guide: top symbols, reading order, entry points, language breakdown. `--write` saves to Markdown |
+| `roam describe [--write] [--force] [-o PATH] [--agent-prompt]` | Auto-generate project description for AI agents. `--write` auto-detects your agent's config file. `--agent-prompt` returns a compact (<500 token) system prompt |
+| `roam agent-export [--format F] [--write]` | Generate agent-context bundle from project analysis (`AGENTS.md` + provider-specific overlays) |
+| `roam minimap [--update] [-o FILE] [--init-notes]` | Compact annotated codebase snapshot for agent config injection: stack, annotated directory tree, key symbols by PageRank, high fan-in symbols to avoid touching, hotspots, conventions. Sentinel-based in-place updates |
+| `roam config [--set-db-dir PATH] [--semantic-backend MODE]` | Manage `.roam/config.json` (DB path, excludes, optional ONNX semantic settings) |
+| `roam map [-n N] [--full] [--budget N]` | Project skeleton: files, languages, entry points, top symbols by PageRank. `--budget` caps output to N tokens |
+| `roam schema [--diff] [--version V]` | JSON envelope schema versioning: view, diff, and validate output schemas |
+| `roam mcp [--list-tools] [--transport T]` | Start MCP server (stdio/SSE/streamable-http), inspect available tools, and expose roam to coding agents |
+| `roam mcp-setup <platform>` | Generate MCP config snippets for AI platforms: claude-code, cursor, windsurf, vscode, gemini-cli, codex-cli |
+
+### Daily Workflow
+
+| Command | Description |
+|---------|-------------|
+| `roam file <path> [--full] [--changed] [--deps-of PATH]` | File skeleton: all definitions with signatures, cognitive load index, health score |
+| `roam symbol <name> [--full]` | Symbol definition + callers + callees + metrics. Supports `file:symbol` disambiguation |
+| `roam context <symbol> [--task MODE] [--for-file PATH]` | AI-optimized context: definition + callers + callees + files-to-read with line ranges |
+| `roam search <pattern> [--kind KIND]` | Find symbols by name pattern, PageRank-ranked |
+| `roam grep <pattern> [-g glob] [-n N]` | Text search annotated with enclosing symbol context |
+| `roam deps <path> [--full]` | What a file imports and what imports it |
+| `roam trace <source> <target> [-k N]` | Dependency paths with coupling strength and hub detection |
+| `roam impact <symbol>` | Blast radius: what breaks if a symbol changes (Personalized PageRank weighted) |
+| `roam diff [--staged] [--full] [REV_RANGE]` | Blast radius of uncommitted changes or a commit range |
+| `roam pr-risk [REV_RANGE]` | PR risk score (0-100, multiplicative model) + structural spread + suggested reviewers |
+| `roam pr-diff [--staged] [--range R] [--format markdown]` | Structural PR diff: metric deltas, edge analysis, symbol changes, footprint. Not text diff — graph delta |
+| `roam api-changes [REV_RANGE]` | API change classifier: breaking/non-breaking changes, severity, and affected contracts |
+| `roam semantic-diff [REV_RANGE]` | Structural change summary: symbols added/removed/modified and changed call edges |
+| `roam test-gaps [REV_RANGE]` | Changed-symbol test gap detection: what changed and what still lacks test coverage |
+| `roam affected [REV_RANGE]` | Monorepo/package impact analysis: what components are affected by a change |
+| `roam attest [REV_RANGE] [--format markdown] [--sign]` | Proof-carrying PR attestation: bundles blast radius, risk, breaking changes, fitness, budget, tests, effects into one verifiable artifact |
+| `roam annotate <symbol> <note>` | Attach persistent notes to symbols (agentic memory across sessions) |
+| `roam annotations [--file F] [--symbol S]` | View stored annotations |
+| `roam diagnose <symbol> [--depth N]` | Root cause analysis: ranks suspects by z-score normalized risk |
+| `roam preflight <symbol\|file>` | Compound pre-change check: blast radius + tests + complexity + coupling + fitness |
+| `roam guard <symbol>` | Compact sub-agent preflight bundle: definition, 1-hop callers/callees, test files, breaking-risk score, and layer signals |
+| `roam agent-plan --agents N` | Decompose partitions into dependency-ordered agent tasks with merge sequencing and handoffs |
+| `roam agent-context --agent-id N [--agents M]` | Generate per-agent execution context: write scope, read-only dependencies, and interface contracts |
+| `roam syntax-check [--changed] [PATHS...]` | Tree-sitter syntax integrity check for changed files and multi-agent judge workflows |
+| `roam verify [--threshold N]` | Pre-commit AI-code consistency check across naming, imports, error handling, and duplication signals |
+| `roam verify-imports [--file F]` | Import hallucination firewall: validate all imports against indexed symbol table, suggest corrections via FTS5 fuzzy matching |
+| `roam safe-delete <symbol>` | Safe deletion check: SAFE/REVIEW/UNSAFE verdict |
+| `roam test-map <name>` | Map a symbol or file to its test coverage |
+| `roam adversarial [--staged] [--range R]` | Adversarial architecture review: generates targeted challenges based on changes |
+| `roam plan [--staged] [--range R] [--agents N]` | Agent work planner: decompose changes into sequenced, dependency-aware steps |
+| `roam closure <symbol> [--rename] [--delete]` | Minimal-change synthesis: all files to touch for a safe rename/delete |
+| `roam mutate move\|rename\|add-call\|extract` | Graph-level code editing: move symbols, rename across codebase, add calls, extract functions. Dry-run by default |
+
+### Codebase Health
+
+| Command | Description |
+|---------|-------------|
+| `roam health [--no-framework] [--gate]` | Composite health score (0-100): weighted geometric mean of tangle ratio, god components, bottlenecks, layer violations. `--gate` runs quality gate checks from `.roam-gates.yml` (exit 5 on failure) |
+| `roam smells [--file F] [--min-severity S]` | Code smell detection: 15 deterministic detectors (brain methods, god classes, feature envy, shotgun surgery, data clumps, etc.) with per-file health scores |
+| `roam dashboard` | Unified single-screen project status: health, hotspots, risks, ownership, and AI-rot indicators |
+| `roam vibe-check [--threshold N]` | AI-rot auditor: 8-pattern taxonomy with composite risk score and prioritized findings |
+| `roam ai-readiness` | 0-100 score for how well this codebase supports AI coding agents |
+| `roam ai-ratio [--since N]` | Statistical estimate of AI-generated code ratio using commit-behavior signals |
+| `roam trends [--record] [--days N] [--metric M]` | Historical metrics snapshots with sparklines and trend deltas |
+| `roam complexity [--bumpy-road]` | Per-function cognitive complexity (SonarSource-compatible, triangular nesting penalty) + Halstead metrics (volume, difficulty, effort, bugs) + cyclomatic density |
+| `roam algo [--task T] [--confidence C] [--profile P]` | Algorithm anti-pattern detection: 23-pattern catalog detects suboptimal algorithms (O(n^2) loops, N+1 queries, quadratic string building, branching recursion, loop-invariant calls) and suggests better approaches with Big-O improvements. Confidence calibration via caller-count + runtime traces, evidence paths, impact scoring, framework-aware N+1 packs, and language-aware fix templates. Alias: `roam math` |
+| `roam n1 [--confidence C] [--verbose]` | Implicit N+1 I/O detection: finds ORM model computed properties (`$appends`/accessors) that trigger lazy-loaded DB queries in collection contexts. Cross-references with eager loading config. Supports Laravel, Django, Rails, SQLAlchemy, JPA |
+| `roam over-fetch [--threshold N] [--confidence C]` | Detect models serializing too many fields: large `$fillable` without `$hidden`/`$visible`, direct controller returns bypassing API Resources, poor exposed-to-hidden ratio |
+| `roam missing-index [--table T] [--confidence C]` | Find queries on non-indexed columns: cross-references `WHERE`/`ORDER BY` clauses, foreign keys, and paginated queries against migration-defined indexes |
+| `roam weather [-n N]` | Hotspots ranked by geometric mean of churn x complexity (percentile-normalized) |
+| `roam debt [--roi]` | Hotspot-weighted tech debt prioritization with SQALE remediation costs and optional refactoring ROI estimates |
+| `roam fitness [--explain]` | Architectural fitness functions from `.roam/fitness.yaml` |
+| `roam alerts` | Health degradation trend detection (Mann-Kendall + Sen's slope) |
+| `roam snapshot [--tag TAG]` | Persist health metrics snapshot for trend tracking |
+| `roam trend` | Health score history with sparkline visualization |
+| `roam digest [--brief] [--since TAG]` | Compare current metrics against last snapshot |
+| `roam forecast [--symbol S] [--horizon N] [--alert-only]` | Predict when metrics will exceed thresholds: Theil-Sen regression on snapshot history + churn-weighted per-symbol risk |
+| `roam budget [--init] [--staged] [--range R]` | Architectural budget enforcement: per-PR delta limits on health, cycles, complexity. CI gate (exit 1 on violation) |
+| `roam bisect [--metric M] [--range R]` | Architectural git bisect: find the commit that degraded a specific metric |
+| `roam ingest-trace <file> [--otel\|--jaeger\|--zipkin\|--generic]` | Ingest runtime trace data (OpenTelemetry, Jaeger, Zipkin) for hotspot overlay |
+| `roam hotspots [--runtime] [--discrepancy]` | Runtime hotspot analysis: find symbols missed by static analysis but critical at runtime |
+
+<details>
+<summary><strong>roam algo — algorithm anti-pattern catalog (23 patterns)</strong></summary>
+
+`roam algo` scans every indexed function against a 23-pattern catalog, ranks findings by runtime-aware impact score, and shows the exact Big-O improvement available. Findings include semantic evidence paths, precision metadata, and language-aware tips/fixes (Python, JS, Go, Rust, Java, etc.):
+
+```
+$ roam algo
+VERDICT: 8 algorithmic improvements found (3 high, 4 medium, 1 low)
+Ordering: highest impact first
+Profile: balanced (filtered 0 low-signal findings)
+
+Nested loop lookup (2):
+  fn   resolve_permissions          src/auth/rbac.py:112     [high, impact=86.4]
+        Current: Nested iteration -- O(n*m)
+        Better:  Hash-map join -- O(n+m)
+        Tip: Build a dict/set from one collection, iterate the other
+
+  fn   find_matching_rule           src/rules/engine.py:67   [high, impact=78.1]
+        Current: Nested iteration -- O(n*m)
+        Better:  Hash-map join -- O(n+m)
+        Tip: Build a dict/set from one collection, iterate the other
+
+String building (1):
+  meth build_query                  src/db/query.py:88       [high, impact=74.0]
+        Current: Loop concatenation -- O(n^2)
+        Better:  Join / StringBuilder -- O(n)
+        Tip: Collect parts in a list, join once at the end
+
+Branching recursion without memoization (1):
+  fn   compute_cost                 src/pricing/calc.py:34   [medium, impact=49.5]
+        Current: Naive branching recursion -- O(2^n)
+        Better:  Memoized / iterative DP -- O(n)
+        Tip: Add @cache / @lru_cache, or convert to iterative with a table
+```
+
+**Full catalog — 23 patterns:**
+
+| Pattern | Anti-pattern detected | Better approach | Improvement |
+|---------|----------------------|-----------------|-------------|
+| Nested loop lookup | `for x in a: for y in b: if x==y` | Hash-map join | O(n·m) → O(n+m) |
+| Membership test | `if x in list` in a loop | Set lookup | O(n) → O(1) per check |
+| Sorting | Bubble / selection sort | Built-in sort | O(n²) → O(n log n) |
+| Search in sorted data | Linear scan on sorted sequence | Binary search | O(n) → O(log n) |
+| String building | `s += chunk` in loop | `join()` / StringBuilder | O(n²) → O(n) |
+| Deduplication | Nested loop dedup | `set()` / `dict.fromkeys` | O(n²) → O(n) |
+| Max / min | Manual tracking loop | `max()` / `min()` | idiom |
+| Accumulation | Manual accumulator | `sum()` / `reduce()` | idiom |
+| Group by key | Manual key-existence check | `defaultdict` / `groupingBy` | idiom |
+| Fibonacci | Naive recursion | Iterative / `@lru_cache` | O(2ⁿ) → O(n) |
+| Exponentiation | Loop multiplication | `pow(b, e, mod)` | O(n) → O(log n) |
+| GCD | Manual loop | `math.gcd()` | O(n) → O(log n) |
+| Matrix multiply | Naive triple loop | NumPy / BLAS | same asymptotic, ~1000× faster via SIMD |
+| Busy wait | `while True: sleep()` poll | Event / condition variable | O(k) → O(1) wake-up |
+| Regex in loop | `re.match()` compiled per iteration | Pre-compiled pattern | O(n·(p+m)) → O(p + n·m) |
+| N+1 query | Per-item DB / API call in loop | Batch `WHERE IN (...)` | n round-trips → 1 |
+| List front operations | `list.insert(0, x)` in loop | `collections.deque` | O(n) → O(1) per op |
+| Sort to select | `sorted(x)[0]` or `sorted(x)[:k]` | `min()` / `heapq.nsmallest` | O(n log n) → O(n) or O(n log k) |
+| Repeated lookup | `.index()` / `.contains()` inside loop | Pre-built set / dict | O(m) → O(1) per lookup |
+| Branching recursion | Naive `f(n-1) + f(n-2)` without cache | `@cache` / iterative DP | O(2ⁿ) → O(n) |
+| Quadratic string building | `result += chunk` across multiple scopes | `parts.append` + `join` at end | O(n²) → O(n) |
+| Loop-invariant call | `get_config()` / `compile_schema()` inside loop body | Hoist before loop | per-iter cost → O(1) |
+| String reversal | Manual char-by-char loop | `s[::-1]` / `.reverse()` | idiom |
+
+**Filtering:**
+
+```bash
+roam algo --task nested-lookup       # one pattern type only
+roam algo --confidence high          # high-confidence findings only
+roam algo --profile strict           # precision-first filtering
+roam algo --task io-in-loop -n 5    # top 5 N+1 query sites
+roam --json algo                     # machine-readable output
+roam --sarif algo > roam-algo.sarif  # SARIF with fingerprints + fixes
+```
+
+**Confidence calibration:** `high` = strong structural signal (unbounded loop + high caller/runtime impact + pattern confirmed); `medium` = pattern matched but uncertainty remains; `low` = heuristic signal only.
+
+**Profiles:** `balanced` (default), `strict` (precision-first), `aggressive` (surface more candidates).
+
+</details>
+
+<details>
+<summary><strong>roam minimap — annotated codebase snapshot for agent configs</strong></summary>
+
+`roam minimap` generates a compact block (stack, annotated directory tree, key symbols, hotspots, conventions) wrapped in sentinel comments for in-place agent config updates:
+
+```
+$ roam minimap
+<!-- roam:minimap generated=2026-02-25 -->
+**Stack:** Python · JavaScript · YAML
+
+```
+.github/  (CI + Action)
+benchmarks/  (agent-eval + oss-eval)
+src/
+  roam/
+    bridges/
+      base.py                 # LanguageBridge
+      registry.py             # register_bridge, detect_bridges
+    commands/  (134 files) # is_test_file, get_changed_files
+    db/
+      connection.py           # find_project_root, batched_in
+      schema.py
+    graph/
+      builder.py              # build_symbol_graph, build_file_graph
+      pagerank.py             # compute_pagerank, compute_centrality
+    languages/  (20 files) # ApexExtractor
+    output/
+      formatter.py            # to_json, json_envelope
+    cli.py                    # cli, LazyGroup
+    mcp_server.py
+tests/  (151 files)
+` ` `
+
+**Key symbols** (PageRank): `open_db` · `ensure_index` · `json_envelope` · `to_json` · `LanguageExtractor`
+
+**Touch carefully** (fan-in >= 15): `to_json` (116 callers) · `json_envelope` (116 callers) · `open_db` (105 callers) · `ensure_index` (100 callers)
+
+**Hotspots** (churn x complexity): `cmd_context.py` · `csharp_lang.py` · `cmd_dead.py`
+
+**Conventions:** snake_case fns, PascalCase classes
+<!-- /roam:minimap -->
+```
+
+**Workflow:**
+
+```bash
+roam minimap                    # print to stdout
+roam minimap --update           # replace sentinel block in CLAUDE.md in-place
+roam minimap -o docs/AGENTS.md  # target a different file
+roam minimap --init-notes       # scaffold .roam/minimap-notes.md for project gotchas
+```
+
+The sentinel pair `<!-- roam:minimap -->` / `<!-- /roam:minimap -->` is replaced on each run — surrounding content is left intact. Add project-specific gotchas to `.roam/minimap-notes.md` and they appear in every subsequent output.
+
+**Tree annotations** come from the top exported symbols by fan-in per file. Non-source root directories (`.github/`, `benchmarks/`, `docs/`) are collapsed immediately. Large subdirectories (e.g. `commands/`, `languages/`) are collapsed at depth 2+ with a file count.
+
+</details>
+
+### Architecture
+
+| Command | Description |
+|---------|-------------|
+| `roam clusters [--min-size N]` | Community detection vs directory structure. Modularity Q-score (Newman 2004) + per-cluster conductance |
+| `roam spectral [--depth N] [--compare] [--gap-only] [--k K]` | Spectral bisection: Fiedler vector partition tree with algebraic connectivity gap verdict |
+| `roam layers` | Topological dependency layers + upward violations + Gini balance |
+| `roam dead [--all] [--summary] [--clusters]` | Unreferenced exported symbols with safety verdicts + confidence scoring (60-95%) |
+| `roam fan [symbol\|file] [-n N] [--no-framework]` | Fan-in/fan-out: most connected symbols or files |
+| `roam risk [-n N] [--domain KW] [--explain]` | Domain-weighted risk ranking |
+| `roam why <name> [name2 ...]` | Role classification (Hub/Bridge/Core/Leaf), reach, criticality |
+| `roam split <file>` | Internal symbol groups with isolation % and extraction suggestions |
+| `roam entry-points` | Entry point catalog with protocol classification |
+| `roam patterns` | Architectural pattern recognition: Strategy, Factory, Observer, etc. |
+| `roam visualize [--format mermaid\|dot] [--focus NAME] [--limit N]` | Generate Mermaid or DOT architecture diagrams. Smart filtering via PageRank, cluster grouping, cycle highlighting |
+| `roam effects [TARGET] [--file F] [--type T]` | Side-effect classification: DB writes, network I/O, filesystem, global mutation. Direct + transitive effects through call graph |
+| `roam dark-matter [--min-cochanges N]` | Detect hidden co-change couplings not explained by import/call edges |
+| `roam simulate move\|extract\|merge\|delete` | Counterfactual architecture simulator: test refactoring ideas in-memory, see metric deltas before writing code |
+| `roam orchestrate --agents N [--files P]` | Multi-agent swarm partitioning: split codebase for parallel agents with zero-conflict guarantees |
+| `roam partition [--agents N]` | Multi-agent partition manifest: conflict risk, complexity, and suggested ownership splits |
+| `roam fingerprint [--compact] [--compare F]` | Topology fingerprint: extract/compare architectural signatures across repos |
+| `roam cut <target> [--depth N]` | Minimum graph cuts: find critical edges whose removal disconnects components |
+| `roam safe-zones` | Graph-based containment boundaries |
+| `roam coverage-gaps` | Unprotected entry points with no path to gate symbols |
+| `roam duplicates [--threshold T] [--min-lines N]` | Semantic duplicate detector: functionally equivalent code clusters with divergent edge-case handling |
+
+### Exploration
+
+| Command | Description |
+|---------|-------------|
+| `roam module <path>` | Directory contents: exports, signatures, dependencies, cohesion |
+| `roam sketch <dir> [--full]` | Compact structural skeleton of a directory |
+| `roam uses <name>` | All consumers: callers, importers, inheritors |
+| `roam owner <path>` | Code ownership: who owns a file or directory |
+| `roam coupling [-n N] [--set]` | Temporal coupling: file pairs that change together (NPMI + lift) |
+| `roam fn-coupling` | Function-level temporal coupling across files |
+| `roam bus-factor [--brain-methods]` | Knowledge loss risk per module |
+| `roam doc-staleness` | Detect stale docstrings |
+| `roam docs-coverage` | Public-symbol doc coverage + stale docs + PageRank-ranked missing-doc hotlist |
+| `roam suggest-refactoring [--limit N] [--min-score N]` | Proactive refactoring recommendations ranked by complexity, coupling, churn, smells, coverage gaps, and debt |
+| `roam plan-refactor <symbol> [--operation auto\|extract\|move]` | Ordered refactor plan with blast radius, test gaps, layer risk, and simulation-based strategy preview |
+| `roam conventions` | Auto-detect naming styles, import preferences. Flags outliers |
+| `roam breaking [REV_RANGE]` | Breaking change detection: removed exports, signature changes |
+| `roam affected-tests <symbol\|file>` | Trace reverse call graph to test files |
+| `roam relate <sym1> <sym2>` | Show relationship between two symbols: shared callers, shortest path, common ancestors |
+| `roam endpoints [--routes] [--api]` | Enumerate all HTTP/API endpoint definitions and surface them for review or cross-repo matching |
+| `roam metrics <file\|symbol>` | Unified vital signs: complexity, fan-in/out, PageRank, churn, test coverage, dead code risk -- all in one call |
+| `roam search-semantic <query>` | Hybrid semantic search: BM25 + TF-IDF + optional local ONNX vectors (select via `--backend`) with framework/library packs |
+| `roam intent [--staged] [--range R]` | Doc-to-code linking: match documentation to symbols, detect drift |
+| `roam x-lang [--bridges] [--edges]` | Cross-language edge browser: inspect bridge-resolved connections |
+
+### Reports & CI
+
+| Command | Description |
+|---------|-------------|
+| `roam report [--list] [--config FILE] [PRESET]` | Compound presets: `first-contact`, `security`, `pre-pr`, `refactor`, `guardian` |
+| `roam describe --write` | Generate agent config (auto-detects: CLAUDE.md, AGENTS.md, .cursor/rules, etc.) |
+| `roam auth-gaps [--routes-only] [--controllers-only] [--min-confidence C]` | Find endpoints missing authentication or authorization: routes outside auth middleware groups, CRUD methods without `$this->authorize()` / `Gate::allows()` checks. String-aware PHP brace parsing |
+| `roam orphan-routes [-n N] [--confidence C]` | Detect backend routes with no frontend consumer: parses route definitions, searches frontend for API call references, reports controller methods with no route mapping |
+| `roam migration-safety [-n N] [--include-archive]` | Detect non-idempotent migrations: missing `hasTable`/`hasColumn` guards, raw SQL without `IF NOT EXISTS`, index operations without existence checks |
+| `roam api-drift [--model M] [--confidence C]` | Detect mismatches between PHP model `$fillable`/`$appends` fields and TypeScript interface properties. Auto-converts snake_case/camelCase for comparison. Single-repo; cross-repo planned for `roam ws api-drift` |
+| `roam codeowners [--unowned] [--owner NAME]` | CODEOWNERS coverage analysis: owned/unowned files, top owners, and ownership risk |
+| `roam drift [--threshold N]` | Ownership drift detection: declared ownership vs observed maintenance activity |
+| `roam suggest-reviewers [REV_RANGE]` | Reviewer recommendation via ownership, recency, breadth, and impact signals |
+| `roam simulate-departure <developer>` | Knowledge-loss simulation: what breaks if a key contributor leaves |
+| `roam dev-profile [--developer NAME] [--since N]` | Developer productivity profile: commit patterns, specialization, impact, and knowledge concentration per contributor |
+| `roam secrets [--fail-on-found] [--include-tests]` | Secret scanning with masking, entropy detection, env-var suppression, remediation suggestions, and optional CI gate failure |
+| `roam vulns [--import-file F] [--reachable-only]` | Vulnerability scanning: ingest npm/pip/trivy/osv reports, auto-detect format, reachability filtering, SARIF output |
+| `roam path-coverage [--from P] [--to P] [--max-depth N]` | Find critical call paths (entry -> sink) with zero test protection. Suggests optimal test insertion points |
+| `roam capsule [--redact-paths] [--no-signatures] [--output F]` | Export sanitized structural graph (no code bodies) for external architectural review |
+| `roam rules [--init] [--ci] [--rules-dir D]` | Plugin DSL for governance: user-defined path/symbol/AST rules via `.roam/rules/` YAML (`$METAVAR` captures supported) |
+| `roam check-rules [--severity S] [--fix]` | Evaluate built-in and user-defined governance rules (10 built-in: no-circular-imports, max-fan-out, etc.) |
+| `roam vuln-map --generic\|--npm-audit\|--trivy F` | Ingest vulnerability reports and match to codebase symbols |
+| `roam vuln-reach [--cve C] [--from E]` | Vulnerability reachability: exact paths from entry points to vulnerable calls |
+| `roam supply-chain [--top N]` | Dependency risk dashboard: pin coverage, risk scoring, supply-chain health |
+| `roam invariants [--staged] [--range R]` | Discover architectural contracts (invariants) from the codebase structure |
+
+### Multi-Repo Workspace
+
+| Command | Description |
+|---------|-------------|
+| `roam ws init <repo1> <repo2> [--name NAME]` | Initialize a workspace from sibling repos. Auto-detects frontend/backend roles |
+| `roam ws status` | Show workspace repos, index ages, cross-repo edge count |
+| `roam ws resolve` | Scan for REST API endpoints and match frontend calls to backend routes |
+| `roam ws understand` | Unified workspace overview: per-repo stats + cross-repo connections |
+| `roam ws health` | Workspace-wide health report with cross-repo coupling assessment |
+| `roam ws context <symbol>` | Cross-repo augmented context: find a symbol across repos + show API callers |
+| `roam ws trace <source> <target>` | Trace cross-repo paths via API edges |
+
+### Global Options
+
+| Option | Description |
+|--------|-------------|
+| `roam --json <command>` | Structured JSON output with consistent envelope |
+| `roam --compact <command>` | Token-efficient output: TSV tables, minimal JSON envelope |
+| `roam --sarif <command>` | SARIF 2.1.0 output for dead, health, complexity, rules, secrets, and algo (GitHub/CI integration) |
+| `roam <command> --gate EXPR` | CI quality gate (e.g., `--gate score>=70`). Exit code 1 on failure |
+
+</details>
+
+## Walkthrough: Investigating a Codebase
+
+<details>
+<summary><strong>10-step walkthrough using Flask as an example</strong> (click to expand)</summary>
+
+Here's how you'd use Roam to understand a project you've never seen before. Using Flask as an example:
+
+**Step 1: Onboard and get the full picture**
+
+```
+$ roam init
+Created .roam/fitness.yaml (6 starter rules)
+Created .github/workflows/roam.yml
+Done. 226 files, 1132 symbols, 233 edges.
+Health: 78/100
+
+$ roam understand
+Tech stack: Python (flask, jinja2, werkzeug)
+Architecture: Monolithic — 3 layers, 5 clusters
+Key abstractions: Flask, Blueprint, Request, Response
+Health: 78/100 — 1 god component (Flask)
+Entry points: src/flask/__init__.py, src/flask/cli.py
+Conventions: snake_case functions, PascalCase classes, relative imports
+Complexity: avg 4.2, 3 high (>15), 0 critical (>25)
+```
+
+**Step 2: Drill into a key file**
+
+```
+$ roam file src/flask/app.py
+src/flask/app.py  (python, 963 lines)
+
+  cls  Flask(App)                                   :76-963
+    meth  __init__(self, import_name, ...)           :152
+    meth  route(self, rule, **options)               :411
+    meth  register_blueprint(self, blueprint, ...)   :580
+    meth  make_response(self, rv)                    :742
+    ...12 more methods
+```
+
+**Step 3: Who depends on this?**
+
+```
+$ roam deps src/flask/app.py
+Imported by:
+file                        symbols
+--------------------------  -------
+src/flask/__init__.py       3
+src/flask/testing.py        2
+tests/test_basic.py         1
+...18 files total
+```
+
+**Step 4: Find the hotspots**
+
+```
+$ roam weather
+=== Hotspots (churn x complexity) ===
+Score  Churn  Complexity  Path                    Lang
+-----  -----  ----------  ----------------------  ------
+18420  460    40.0        src/flask/app.py        python
+12180  348    35.0        src/flask/blueprints.py python
+```
+
+**Step 5: Check architecture health**
+
+```
+$ roam health
+Health: 78/100
+  Tangle: 0.0% (0/1132 symbols in cycles)
+  1 god component (Flask, degree 47, actionable)
+  0 bottlenecks, 0 layer violations
+
+=== God Components (degree > 20) ===
+Sev      Name   Kind  Degree  Cat  File
+-------  -----  ----  ------  ---  ------------------
+WARNING  Flask  cls   47      act  src/flask/app.py
+```
+
+**Step 6: Get AI-ready context for a symbol**
+
+```
+$ roam context Flask
+Files to read:
+  src/flask/app.py:76-963              # definition
+  src/flask/__init__.py:1-15           # re-export
+  src/flask/testing.py:22-45           # caller: FlaskClient.__init__
+  tests/test_basic.py:12-30            # caller: test_app_factory
+  ...12 more files
+
+Callers: 47  Callees: 3
+```
+
+**Step 7: Pre-change safety check**
+
+```
+$ roam preflight Flask
+=== Preflight: Flask ===
+Blast radius: 47 callers, 89 transitive
+Affected tests: 31 (DIRECT: 12, TRANSITIVE: 19)
+Complexity: cc=40 (critical), nesting=6
+Coupling: 3 hidden co-change partners
+Fitness: 1 violation (max-complexity exceeded)
+Verdict: HIGH RISK — consider splitting before modifying
+```
+
+**Step 8: Decompose a large file**
+
+```
+$ roam split src/flask/app.py
+=== Split analysis: src/flask/app.py ===
+  87 symbols, 42 internal edges, 95 external edges
+  Cross-group coupling: 18%
+
+  Group 1 (routing) — 12 symbols, isolation: 83% [extractable]
+    meth  route              L411  PR=0.0088
+    meth  add_url_rule       L450  PR=0.0045
+    ...
+
+=== Extraction Suggestions ===
+  Extract 'routing' group: route, add_url_rule, endpoint (+9 more)
+    83% isolated, only 3 edges to other groups
+```
+
+**Step 9: Understand why a symbol matters**
+
+```
+$ roam why Flask url_for Blueprint
+Symbol     Role          Fan         Reach     Risk      Verdict
+---------  ------------  ----------  --------  --------  --------------------------------------------------
+Flask      Hub           fan-in:47   reach:89  CRITICAL  God symbol (47 in, 12 out). Consider splitting.
+url_for    Core utility  fan-in:31   reach:45  HIGH      Widely used utility (31 callers). Stable interface.
+Blueprint  Bridge        fan-in:18   reach:34  moderate  Coupling point between clusters.
+```
+
+**Step 10: Generate docs and set up CI**
+
+```
+$ roam describe --write
+Wrote CLAUDE.md (98 lines)  # auto-detects: CLAUDE.md, AGENTS.md, .cursor/rules, etc.
+
+$ roam health --gate score>=70
+Health: 78/100 — PASS
+```
+
+Ten commands. Complete picture: structure, dependencies, hotspots, health, context, safety checks, decomposition, and CI gates.
+
+</details>
+
+## Integration with AI Coding Tools
+
+Roam is designed to be called by coding agents via shell commands. Instead of repeatedly grepping and reading files, the agent runs one `roam` command and gets structured output.
+
+**Decision order for agents:**
+
+| Situation | Command |
+|-----------|---------|
+| First time in a repo | `roam understand` then `roam tour` |
+| Need to modify a symbol | `roam preflight <name>` (blast radius + tests + fitness) |
+| Debugging a failure | `roam diagnose <name>` (root cause ranking) |
+| Need files to read | `roam context <name>` (files + line ranges) |
+| Need to find a symbol | `roam search <pattern>` |
+| Need file structure | `roam file <path>` |
+| Pre-PR check | `roam pr-risk HEAD~3..HEAD` |
+| What breaks if I change X? | `roam impact <symbol>` |
+| Check for N+1 queries | `roam n1` (implicit lazy-load detection) |
+| Check auth coverage | `roam auth-gaps` (routes + controllers) |
+| Check migration safety | `roam migration-safety` (idempotency guards) |
+
+**Fastest setup:**
+
+```bash
+roam describe --write               # auto-detects your agent's config file
+roam describe --write -o AGENTS.md  # or specify an explicit path
+roam describe --agent-prompt        # compact ~500-token prompt (append to any config)
+roam minimap --update               # inject/refresh annotated codebase minimap in CLAUDE.md
+```
+
+**Agent not using Roam correctly?** If your agent is ignoring Roam and falling back to grep/read exploration, it likely doesn't have the instructions. Run:
+
+```bash
+roam describe --write          # writes instructions to your agent's config (CLAUDE.md, AGENTS.md, etc.)
+```
+
+If you already have a config file and don't want to overwrite it:
+
+```bash
+roam describe --agent-prompt   # prints a compact prompt — copy-paste into your existing config
+roam minimap --update          # injects an annotated codebase snapshot into CLAUDE.md (won't touch other content)
+```
+
+This teaches the agent which Roam command to use for each situation (e.g., `roam preflight` before changes, `roam context` for files to read, `roam diagnose` for debugging).
+
+<details>
+<summary><strong>Copy-paste agent instructions</strong></summary>
+
+```markdown
+## Codebase navigation
+
+This project uses `roam` for codebase comprehension. Always prefer roam over Glob/Grep/Read exploration.
+
+Before modifying any code:
+1. First time in the repo: `roam understand` then `roam tour`
+2. Find a symbol: `roam search <pattern>`
+3. Before changing a symbol: `roam preflight <name>` (blast radius + tests + fitness)
+4. Need files to read: `roam context <name>` (files + line ranges, prioritized)
+5. Debugging a failure: `roam diagnose <name>` (root cause ranking)
+6. After making changes: `roam diff` (blast radius of uncommitted changes)
+
+Additional: `roam health` (0-100 score), `roam impact <name>` (what breaks),
+`roam pr-risk` (PR risk), `roam file <path>` (file skeleton).
+
+Run `roam --help` for all commands. Use `roam --json <cmd>` for structured output.
+```
+
+</details>
+
+<details>
+<summary><strong>Where to put this for each tool</strong></summary>
+
+| Tool | Config file |
+|------|-------------|
+| **Claude Code** | `CLAUDE.md` in your project root |
+| **OpenAI Codex CLI** | `AGENTS.md` in your project root |
+| **Gemini CLI** | `GEMINI.md` in your project root |
+| **Cursor** | `.cursor/rules/roam.mdc` (add `alwaysApply: true` frontmatter) |
+| **Windsurf** | `.windsurf/rules/roam.md` (add `trigger: always_on` frontmatter) |
+| **GitHub Copilot** | `.github/copilot-instructions.md` |
+| **Aider** | `CONVENTIONS.md` |
+| **Continue.dev** | `config.yaml` rules |
+| **Cline** | `.clinerules/` directory |
+
+</details>
+
+<details>
+<summary><strong>Roam vs native tools</strong></summary>
+
+| Task | Use Roam | Use native tools |
+|------|----------|-----------------|
+| "What calls this function?" | `roam symbol <name>` | LSP / Grep |
+| "What files do I need to read?" | `roam context <name>` | Manual tracing (5+ calls) |
+| "Is it safe to change X?" | `roam preflight <name>` | Multiple manual checks |
+| "Show me this file's structure" | `roam file <path>` | Read the file directly |
+| "Understand project architecture" | `roam understand` | Manual exploration |
+| "What breaks if I change X?" | `roam impact <symbol>` | No direct equivalent |
+| "What tests to run?" | `roam affected-tests <name>` | Grep for imports (misses indirect) |
+| "What's causing this bug?" | `roam diagnose <name>` | Manual call-chain tracing |
+| "Codebase health score for CI" | `roam health --gate score>=70` | No equivalent |
+
+</details>
+
+## MCP Server
+
+Roam includes a [Model Context Protocol](https://modelcontextprotocol.io/) server for direct integration with tools that support MCP.
+
+```bash
+pip install "roam-code[mcp]"
+roam mcp
+```
+
+101 tools, 10 resources, and 5 prompts are available in the full preset. Most tools are read-only index queries; side-effect tools are explicitly annotated.
+
+**MCP v2 highlights (v11):**
+- In-process MCP execution (no subprocess shell-out per call)
+- Preset-based tool surfacing (`core`, `review`, `refactor`, `debug`, `architecture`, `full`)
+- Compound tools that collapse multi-step exploration/review flows into one call
+- Structured output schemas + tool annotations for safer planner behavior
+
+**Default preset:** `core` (24 tools: 23 core + `roam_expand_toolset` meta-tool).
+
+```bash
+# Default
+roam mcp
+
+# Full toolset
+ROAM_MCP_PRESET=full roam mcp
+
+# Legacy compatibility (same as full preset)
+ROAM_MCP_LITE=0 roam mcp
+```
+
+Core preset tools: `roam_affected_tests`, `roam_batch_get`, `roam_batch_search`, `roam_complexity_report`, `roam_context`, `roam_dead_code`, `roam_deps`, `roam_diagnose`, `roam_diagnose_issue`, `roam_diff`, `roam_expand_toolset`, `roam_explore`, `roam_file_info`, `roam_health`, `roam_impact`, `roam_pr_risk`, `roam_preflight`, `roam_prepare_change`, `roam_review_change`, `roam_search_symbol`, `roam_syntax_check`, `roam_trace`, `roam_understand`, `roam_uses`.
+
+<details>
+<summary><strong>MCP tool list (all 101)</strong></summary>
+
+| Tool | Description |
+|------|-------------|
+| `roam_understand` | Full codebase briefing |
+| `roam_health` | Health score (0-100) + issues |
+| `roam_preflight` | Pre-change safety check |
+| `roam_search_symbol` | Find symbols by name |
+| `roam_context` | Files-to-read for modifying a symbol |
+| `roam_trace` | Dependency path between two symbols |
+| `roam_impact` | Blast radius of changing a symbol |
+| `roam_file_info` | File skeleton with all definitions |
+| `roam_pr_risk` | Risk score for pending changes |
+| `roam_breaking_changes` | Detect breaking changes between refs |
+| `roam_affected_tests` | Find tests affected by a change |
+| `roam_dead_code` | List unreferenced exports |
+| `roam_complexity_report` | Per-symbol cognitive complexity |
+| `roam_repo_map` | Project skeleton with key symbols |
+| `roam_tour` | Auto-generated onboarding guide |
+| `roam_diagnose` | Root cause analysis for debugging |
+| `roam_visualize` | Generate Mermaid or DOT architecture diagrams |
+| `roam_algo` | Algorithm anti-pattern detection with language-aware tips |
+| `roam_ws_understand` | Unified multi-repo workspace overview |
+| `roam_ws_context` | Cross-repo augmented symbol context |
+| `roam_pr_diff` | Structural PR diff: metric deltas, edge analysis, symbol changes |
+| `roam_budget_check` | Check changes against architectural budgets |
+| `roam_effects` | Side-effect classification (DB writes, network, filesystem) |
+| `roam_attest` | Proof-carrying PR attestation with all evidence bundled |
+| `roam_capsule_export` | Export sanitized structural graph (no code bodies) |
+| `roam_path_coverage` | Find critical untested call paths (entry -> sink) |
+| `roam_forecast` | Predict when metrics will exceed thresholds |
+| `roam_simulate` | Counterfactual architecture simulator |
+| `roam_orchestrate` | Multi-agent swarm partitioning |
+| `roam_fingerprint` | Topology fingerprint comparison |
+| `roam_mutate` | Graph-level code editing (move/rename/extract) |
+| `roam_dark_matter` | Hidden co-change coupling detection |
+| `roam_closure` | Minimal-change synthesis for rename/delete |
+| `roam_adversarial_review` | Adversarial architecture review |
+| `roam_generate_plan` | Agent work planner |
+| `roam_get_invariants` | Architectural invariant discovery |
+| `roam_bisect_blame` | Architectural git bisect |
+| `roam_doc_intent` | Doc-to-code linking |
+| `roam_cut_analysis` | Minimum graph cut analysis |
+| `roam_annotate_symbol` | Attach persistent notes to symbols |
+| `roam_get_annotations` | View stored annotations |
+| `roam_relate` | Show relationship between two symbols |
+| `roam_search_semantic` | Semantic search by meaning |
+| `roam_rules_check` | Plugin DSL governance rules |
+| `roam_check_rules` | Built-in + user-defined governance rule evaluation with autofix templates |
+| `roam_supply_chain` | Dependency risk dashboard: pin coverage and supply-chain health |
+| `roam_spectral` | Spectral bisection: Fiedler vector partition tree and modularity gap |
+| `roam_vuln_map` | Vulnerability report ingestion |
+| `roam_vuln_reach` | Vulnerability reachability paths |
+| `roam_ingest_trace` | Ingest runtime trace data |
+| `roam_runtime_hotspots` | Runtime hotspot analysis |
+| `roam_diff` | Blast radius of uncommitted/committed changes |
+| `roam_symbol` | Symbol definition, callers, callees, metrics |
+| `roam_deps` | File-level import/imported-by relationships |
+| `roam_uses` | All consumers of a symbol by edge type |
+| `roam_weather` | Code hotspots: churn x complexity ranking |
+| `roam_debt` | Hotspot-weighted technical debt prioritization with optional ROI estimate |
+| `roam_docs_coverage` | Doc coverage and stale-doc drift with PageRank-ranked missing docs |
+| `roam_suggest_refactoring` | Rank proactive refactoring candidates using complexity, coupling, churn, smells, and coverage gaps |
+| `roam_plan_refactor` | Build an ordered refactor plan for one symbol with risk/test/simulation context |
+| `roam_n1` | Detect N+1 I/O patterns in ORM code |
+| `roam_auth_gaps` | Find endpoints missing auth |
+| `roam_over_fetch` | Detect models serializing too many fields |
+| `roam_missing_index` | Find queries on non-indexed columns |
+| `roam_orphan_routes` | Detect dead backend routes |
+| `roam_migration_safety` | Detect non-idempotent migrations |
+| `roam_api_drift` | Backend/frontend model mismatch detection |
+| `roam_expand_toolset` | Discover presets, active toolset, and switch instructions |
+| `roam_explore` | Compound first-contact exploration bundle for fast repo orientation |
+| `roam_prepare_change` | Compound pre-change bundle: context, blast radius, risk, and tests |
+| `roam_review_change` | Compound review bundle for changed code and architecture checks |
+| `roam_diagnose_issue` | Compound debugging bundle with ranked suspects and dependency context |
+| `roam_onboard` | Structured onboarding brief for new contributors/agents |
+| `roam_syntax_check` | Tree-sitter syntax integrity validation for changed paths |
+| `roam_agent_export` | Generate multi-agent instruction bundles (`AGENTS.md` + overlays) |
+| `roam_vibe_check` | AI-rot auditor with 8-pattern taxonomy and composite score |
+| `roam_ai_readiness` | AI-agent effectiveness readiness scoring and recommendations |
+| `roam_dashboard` | Unified status snapshot across health, risk, churn, and quality |
+| `roam_codeowners` | CODEOWNERS coverage analysis and unowned file discovery |
+| `roam_drift` | Ownership drift detection from declared vs observed ownership |
+| `roam_suggest_reviewers` | Reviewer recommendations with multi-signal scoring |
+| `roam_simulate_departure` | Knowledge-loss simulation for contributor departure scenarios |
+| `roam_verify` | Pre-commit consistency verification and policy checks |
+| `roam_api_changes` | API signature change classification and severity labeling |
+| `roam_test_gaps` | Changed-symbol test gap analysis |
+| `roam_ai_ratio` | Estimated AI-generated code ratio from repository signals |
+| `roam_duplicates` | Semantic duplicate detection across structurally similar functions |
+| `roam_partition` | Multi-agent partition manifest with conflict and complexity scores |
+| `roam_affected` | Monorepo/package affected-set analysis for diffs |
+| `roam_semantic_diff` | Structural diff of symbol/edge changes |
+| `roam_trends` | Historical metric trend retrieval with sparkline output |
+| `roam_secrets` | Secret scanning with masking and CI-friendly fail behavior |
+| `roam_endpoints` | Enumerate HTTP/API endpoint definitions across the codebase |
+| `roam_doctor` | Diagnose installation and environment health |
+| `roam_init` | Initialize roam workspace state and build the first index |
+| `roam_reindex` | Refresh or force-rebuild the index with task-mode support |
+| `roam_reset` | Reset the roam index and cached data |
+| `roam_clean` | Remove stale or orphaned index entries |
+| `roam_batch_search` | Batch symbol search: run multiple pattern queries in a single call |
+| `roam_batch_get` | Batch context retrieval: fetch multiple symbols/files in a single call |
+| `roam_dev_profile` | Developer productivity profile: commit patterns, specialization, and impact |
+
+**Resources:** `roam://health` (current health score), `roam://summary` (project overview)
+
+</details>
+
+<details>
+<summary><strong>Claude Code</strong></summary>
+
+```bash
+claude mcp add roam-code -- roam mcp
+```
+
+Or add to `.mcp.json` in your project root:
+
+```json
+{
+  "mcpServers": {
+    "roam-code": {
+      "command": "roam",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+</details>
+
+<details>
+<summary><strong>Claude Desktop</strong></summary>
+
+Add to your `claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "roam-code": {
+      "command": "roam",
+      "args": ["mcp"],
+      "cwd": "/path/to/your/project"
+    }
+  }
+}
+```
+
+</details>
+
+<details>
+<summary><strong>Cursor</strong></summary>
+
+Add to `.cursor/mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "roam-code": {
+      "command": "roam",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+</details>
+
+<details>
+<summary><strong>VS Code + Copilot</strong></summary>
+
+Add to `.vscode/mcp.json`:
+
+```json
+{
+  "servers": {
+    "roam-code": {
+      "type": "stdio",
+      "command": "roam",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+</details>
+
+## CI/CD Integration
+
+All you need is Python 3.9+ and `pip install roam-code`.
+
+### GitHub Actions
+
+```yaml
+# .github/workflows/roam.yml
+name: Roam Analysis
+on: [pull_request]
+
+jobs:
+  roam:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: Cranot/roam-code@main
+        with:
+          command: health --gate score>=70
+          comment: true
+          fail-on-violation: true
+```
+
+Use `roam init` to auto-generate this workflow.
+
+| Input | Default | Description |
+|-------|---------|-------------|
+| `command` | `health` | Roam command to run |
+| `python-version` | `3.12` | Python version |
+| `comment` | `false` | Post results as PR comment |
+| `fail-on-violation` | `false` | Fail the job on violations |
+| `roam-version` | (latest) | Pin to a specific version |
+
+<details>
+<summary><strong>GitLab CI</strong></summary>
+
+```yaml
+roam-analysis:
+  stage: test
+  image: python:3.12-slim
+  before_script:
+    - pip install roam-code
+  script:
+    - roam index
+    - roam health --gate score>=70
+    - roam --json pr-risk origin/main..HEAD > roam-report.json
+  artifacts:
+    paths:
+      - roam-report.json
+  rules:
+    - if: $CI_MERGE_REQUEST_IID
+```
+
+</details>
+
+<details>
+<summary><strong>Azure DevOps / any CI</strong></summary>
+
+Universal pattern:
+
+```bash
+pip install roam-code
+roam index
+roam health --gate score>=70    # exit 1 on failure
+roam --json health > report.json
+```
+
+</details>
+
+## SARIF Output
+
+Roam exports analysis results in [SARIF 2.1.0](https://sarifweb.azurewebsites.net/) format for GitHub Code Scanning.
+
+```python
+from roam.output.sarif import health_to_sarif, write_sarif
+
+sarif = health_to_sarif(health_data)
+write_sarif(sarif, "roam-health.sarif")
+```
+
+```yaml
+- uses: github/codeql-action/upload-sarif@v3
+  with:
+    sarif_file: roam-health.sarif
+```
+
+## For Teams
+
+Zero infrastructure, zero vendor lock-in, zero data leaving your network.
+
+| Tool | Annual cost (20-dev team) | Infrastructure | Setup time |
+|------|--------------------------|----------------|------------|
+| SonarQube Server | $15,000-$45,000 | Self-hosted server | Days |
+| CodeScene | $20,000-$60,000 | SaaS or on-prem | Hours |
+| Code Climate | $12,000-$36,000 | SaaS | Hours |
+| **Roam** | **$0 (MIT license)** | **None (local)** | **5 minutes** |
+
+<details>
+<summary><strong>Team rollout guide</strong></summary>
+
+**Week 1-2 (pilot):** 1-2 developers run `roam init` on one repo. Use `roam preflight` before changes, `roam pr-risk` before PRs.
+
+**Week 3-4 (expand):** Add `roam health --gate score>=60` to CI as a non-blocking check.
+
+**Month 2+ (standardize):** Tighten to `--gate score>=70`. Expand to additional repos. Track trajectory with `roam trend`.
+
+</details>
+
+<details>
+<summary><strong>Complements your existing stack</strong></summary>
+
+| If you use... | Roam adds... |
+|---------------|-------------|
+| **SonarQube** | Architecture-level analysis: dependency cycles, god components, blast radius, health scoring |
+| **CodeScene** | Free, local alternative for health scoring and hotspot analysis |
+| **ESLint / Pylint** | Cross-language architecture checks. Linters enforce style per file; Roam enforces architecture across the codebase |
+| **LSP** | AI-agent-optimized queries. `roam context` answers "what calls this?" with PageRank-ranked results in one call |
+
+</details>
+
+## Language Support
+
+### Tier 1 -- Full extraction (dedicated parsers)
+
+| Language | Extensions | Symbols | References | Inheritance |
+|----------|-----------|---------|------------|-------------|
+| Python | `.py` `.pyi` | classes, functions, methods, decorators, variables | imports, calls, inheritance | extends, `__all__` exports |
+| JavaScript | `.js` `.jsx` `.mjs` `.cjs` | classes, functions, arrow functions, CJS exports | imports, require(), calls | extends |
+| TypeScript | `.ts` `.tsx` `.mts` `.cts` | interfaces, type aliases, enums + all JS | imports, calls, type refs | extends, implements |
+| Java | `.java` | classes, interfaces, enums, constructors, fields | imports, calls | extends, implements |
+| Go | `.go` | structs, interfaces, functions, methods, fields | imports, calls | embedded structs |
+| Rust | `.rs` | structs, traits, impls, enums, functions | use, calls | impl Trait for Struct |
+| C / C++ | `.c` `.h` `.cpp` `.hpp` `.cc` | structs, classes, functions, namespaces, templates | includes, calls | extends |
+| C# | `.cs` | classes, interfaces, structs, enums, records, methods, constructors, properties, delegates, events, fields | using directives, calls, `new`, attributes | extends, implements |
+| PHP | `.php` | classes, interfaces, traits, enums, methods, properties | namespace use, calls, static calls, `new` | extends, implements, use (traits) |
+| Visual FoxPro | `.prg` | functions, procedures, classes, methods, properties, constants | DO, SET PROCEDURE/CLASSLIB, CREATEOBJECT, `=func()`, `obj.method()` | DEFINE CLASS ... AS |
+| YAML (CI/CD) | `.yml` `.yaml` | GitLab CI: jobs, template anchors, stages. GitHub Actions: workflow name, jobs, reusable workflows. Generic: top-level keys | `extends:`, `needs:`, `!reference`, `uses:` | — |
+| HCL / Terraform | `.tf` `.tfvars` `.hcl` | `resource`, `data`, `variable`, `output`, `module`, `provider`, `locals` entries | `var.*`, `module.*`, `data.*`, `local.*`, resource cross-refs | — |
+| Vue | `.vue` | via `<script>` block extraction (TS/JS) | imports, calls, type refs | extends, implements |
+| Svelte | `.svelte` | via `<script>` block extraction (TS/JS) | imports, calls, type refs | extends, implements |
+
+<details>
+<summary><strong>Salesforce ecosystem (Tier 1)</strong></summary>
+
+| Language | Extensions | Symbols | References |
+|----------|-----------|---------|------------|
+| Apex | `.cls` `.trigger` | classes, triggers, SOQL, annotations | imports, calls, System.Label, generic type refs |
+| Aura | `.cmp` `.app` `.evt` `.intf` `.design` | components, attributes, methods, events | controller refs, component refs |
+| LWC (JavaScript) | `.js` (in LWC dirs) | anonymous class from filename | `@salesforce/apex/`, `@salesforce/schema/`, `@salesforce/label/` |
+| Visualforce | `.page` `.component` | pages, components | controller/extensions, merge fields, includes |
+| SF Metadata XML | `*-meta.xml` | objects, fields, rules, layouts | Apex class refs, formula field refs, Flow actionCalls |
+
+Cross-language edges mean `roam impact AccountService` shows blast radius across Apex, LWC, Aura, Visualforce, and Flows.
+
+</details>
+
+| Ruby | `.rb` | classes, modules, methods, singleton methods, constants | require, require_relative, include/extend, calls, ClassName.new | class inheritance |
+| JSONC | `.jsonc` | via JSON grammar | -- | -- |
+| MDX | `.mdx` | via Markdown grammar | -- | -- |
+
+### Tier 2 -- Generic extraction
+
+Kotlin (`.kt` `.kts`), Swift (`.swift`), Scala (`.scala` `.sc`)
+
+Tier 2 languages get symbol extraction and basic inheritance via a generic tree-sitter walker.
+
+## Performance
+
+| Metric | Value |
+|--------|-------|
+| Index 200 files | ~3-5s |
+| Index 3,000 files | ~2 min |
+| Incremental (no changes) | <1s |
+| Any query command | <0.5s |
+
+<details>
+<summary><strong>Detailed benchmarks</strong></summary>
+
+### Indexing Speed
+
+| Project | Language | Files | Symbols | Edges | Index Time | Rate |
+|---------|----------|-------|---------|-------|-----------|------|
+| Express | JS | 211 | 624 | 804 | 3s | 70 files/s |
+| Axios | JS | 237 | 1,065 | 868 | 6s | 41 files/s |
+| Vue | TS | 697 | 5,335 | 8,984 | 25s | 28 files/s |
+| Laravel | PHP | 3,058 | 39,097 | 38,045 | 1m46s | 29 files/s |
+| Svelte | TS | 8,445 | 16,445 | 19,618 | 2m40s | 52 files/s |
+
+### Quality Benchmark
+
+| Repo | Language | Score | Coverage | Edge Density |
+|------|----------|-------|----------|--------------|
+| Laravel | PHP | **9.55** | 91.2% | 0.97 |
+| Vue | TS | **9.27** | 85.8% | 1.68 |
+| Svelte | TS | **9.04** | 94.7% | 1.19 |
+| Axios | JS | **8.98** | 85.9% | 0.82 |
+| Express | JS | **8.46** | 96.0% | 1.29 |
+
+### Token Efficiency
+
+| Metric | Value |
+|--------|-------|
+| 1,600-line file → `roam file` | ~5,000 chars (~70:1 compression) |
+| Full project map | ~4,000 chars |
+| `--compact` mode | 40-50% additional token reduction |
+| `roam preflight` replaces | 5-7 separate agent tool calls |
+
+</details>
+
+Agent-efficiency benchmarks: see the [`benchmarks/`](benchmarks/) directory for harness, repos, and results.
+
+## How It Works
+
+```
+Codebase
+    |
+[1] Discovery ──── git ls-files (respects .gitignore + .roamignore)
+    |
+[2] Parse ──────── tree-sitter AST per file (26 languages)
+    |
+[3] Extract ────── symbols + references (calls, imports, inheritance)
+    |
+[4] Resolve ────── match references to definitions → edges
+    |
+[5] Metrics ────── adaptive PageRank, betweenness, cognitive complexity, Halstead
+    |
+[6] Algorithms ── 23-pattern anti-pattern catalog (O(n^2) loops, N+1, recursion)
+    |
+[7] Git ────────── churn, co-change matrix, authorship, Renyi entropy
+    |
+[8] Clusters ───── Louvain community detection
+    |
+[9] Health ─────── per-file scores (7-factor) + composite score (0-100)
+    |
+[10] Store ─────── .roam/index.db (SQLite, WAL mode)
+```
+
+After the first full index, `roam index` only re-processes changed files (mtime + SHA-256 hash). Incremental updates are near-instant.
+
+<details>
+<summary><strong>Graph algorithms</strong></summary>
+
+- **Adaptive PageRank** -- damping factor auto-tunes based on cycle density (0.82-0.92); identifies the most important symbols (used by `map`, `search`, `context`)
+- **Personalized PageRank** -- distance-weighted blast radius for `impact` (Gleich, 2015)
+- **Adaptive betweenness centrality** -- exact for small graphs, sqrt-scaled sampling for large (Brandes & Pich, 2007); finds bottleneck symbols
+- **Edge betweenness centrality** -- identifies critical cycle-breaking edges in SCCs (Brandes, 2001)
+- **Tarjan's SCC** -- detects dependency cycles with tangle ratio
+- **Propagation Cost** -- fraction of system affected by any change, via transitive closure (MacCormack, Rusnak & Baldwin, 2006)
+- **Algebraic connectivity (Fiedler value)** -- second-smallest Laplacian eigenvalue; measures architectural robustness (Fiedler, 1973)
+- **Louvain community detection** -- groups related symbols into clusters
+- **Modularity Q-score** -- measures if cluster boundaries match natural community structure (Newman, 2004)
+- **Conductance** -- per-cluster boundary tightness: cut(S, S_bar) / min(vol(S), vol(S_bar)) (Yang & Leskovec)
+- **Topological sort** -- computes dependency layers, Gini coefficient for layer balance (Gini, 1912), weighted violation severity
+- **k-shortest simple paths** -- traces dependency paths with coupling strength
+- **Renyi entropy (order 2)** -- measures co-change distribution; more robust to outliers than Shannon (Renyi, 1961)
+- **Mann-Kendall trend test** -- non-parametric degradation detection, robust to noise (Mann, 1945; Kendall, 1975)
+- **Sen's slope estimator** -- robust trend magnitude, resistant to outliers (Sen, 1968)
+- **NPMI** -- Normalized Pointwise Mutual Information for coupling strength (Bouma, 2009)
+- **Lift** -- association rule mining metric for co-change statistical significance (Agrawal & Srikant, 1994)
+- **Halstead metrics** -- volume, difficulty, effort, and predicted bugs from operator/operand counts (Halstead, 1977)
+- **SQALE remediation cost** -- time-to-fix estimates per issue type for tech debt prioritization (Letouzey, 2012)
+- **Algorithm anti-pattern catalog** -- 23 patterns detecting suboptimal algorithms (quadratic loops, N+1 queries, quadratic string building, branching recursion, manual top-k, loop-invariant calls) with confidence calibration via caller-count and bounded-loop analysis
+
+</details>
+
+<details>
+<summary><strong>Health scoring</strong></summary>
+
+Composite health score (0-100) using a **weighted geometric mean** of sigmoid health factors. Non-compensatory: a zero in any dimension cannot be masked by high scores in others.
+
+| Factor | Weight | What it measures |
+|--------|--------|-----------------|
+| Tangle ratio | 30% | % of symbols in dependency cycles |
+| God components | 20% | Symbols with extreme fan-in/fan-out |
+| Bottlenecks | 15% | High-betweenness chokepoints |
+| Layer violations | 15% | Upward dependency violations (severity-weighted by layer distance) |
+| Per-file health | 20% | Average of 7-factor file health scores |
+
+Each factor uses sigmoid health: `h = e^(-signal/scale)` (1 = pristine, approaches 0 = worst). Score = `100 * product(h_i ^ w_i)`. Also reports **propagation cost** (MacCormack 2006) and **algebraic connectivity** (Fiedler 1973). Per-file health (1-10) combines: cognitive complexity (triangular nesting penalty per Sweller's Cognitive Load Theory), indentation complexity, cycle membership, god component membership, dead export ratio, co-change entropy, and churn amplification.
+
+</details>
+
+## How Roam Compares
+
+roam-code is the only tool that combines graph algorithms (PageRank, Tarjan SCC, Louvain clustering), git archaeology, architecture simulation, and multi-agent partitioning in a single local CLI with zero API keys.
+
+Documentation (local HTML in `docs/site/`, CI-deployed via `.github/workflows/pages.yml`):
+- `docs/site/getting-started.html` — tutorial
+- `docs/site/command-reference.html` — examples
+- `docs/site/architecture.html` — diagram + internals
+- `docs/site/landscape.html` — competitor matrix
+
+| Capability | roam-code | AI IDEs (Cursor, Windsurf) | AI Agents (Claude Code, Codex) | SAST (SonarQube, CodeQL) |
+|---|---|---|---|---|
+| Persistent local index | SQLite | Cloud embeddings | None | Per-scan |
+| Call graph analysis | Yes | No | No | Yes (CodeQL) |
+| PageRank / centrality | Yes | No | No | No |
+| Cycle detection (Tarjan) | Yes | No | No | Deprecated (SonarQube) |
+| Community detection (Louvain) | Yes | No | No | No |
+| Git churn / co-change | Yes | No | No | No |
+| Architecture simulation | Yes | No | No | No |
+| Multi-agent partitioning | Yes | No | No | No |
+| MCP tools for agents | 101 (24 in default core preset) | Client only | Client only | 34 (SonarQube) |
+| Languages | 26 | 70+ | 50+ | 12-42 |
+| 100% local, zero API keys | Yes | No | No | Partial |
+| Open source | MIT | No | Partial | Partial |
+
+### Key Differentiators
+
+- **vs AI IDEs** (Cursor, Windsurf, Augment): roam-code provides deterministic structural analysis. AI IDEs use probabilistic embeddings that can't guarantee reproducible results.
+- **vs AI Agents** (Claude Code, Codex CLI, Gemini CLI): These agents read files one at a time. roam-code pre-computes relationships so agents get instant answers about architecture, blast radius, and dependencies.
+- **vs SAST Tools** (SonarQube, CodeQL, Semgrep): SAST tools find bugs and vulnerabilities. roam-code understands architecture -- how code is structured, where it's coupled, and what breaks when you change it. Complementary, not competitive.
+- **vs Code Search** (Sourcegraph/Amp, Greptile): Text search finds where code is. roam-code understands why code matters -- which functions are central, which modules are tangled, which files are high-risk.
+
+## FAQ
+
+**Does Roam send any data externally?**
+No. Zero network calls. No telemetry, no analytics, no update checks.
+
+**Can Roam run in air-gapped environments?**
+Yes. Once installed, no internet access is required.
+
+**Does Roam modify my source code?**
+Read-only by default. Creates `.roam/` with an index database. The `roam mutate` command can apply code changes (move/rename/extract) but defaults to `--dry-run` mode — you must explicitly pass `--apply` to write changes.
+
+**How does Roam handle monorepos?**
+Indexes from the root. Batched SQL handles 100k+ symbols. Incremental updates stay fast.
+
+**How does Roam handle multi-repo projects (e.g., frontend + backend)?**
+Use `roam ws init <repo1> <repo2>` to create a workspace. Each repo keeps its own index; a workspace overlay DB stores cross-repo API edges. `roam ws resolve` scans for REST endpoints and matches frontend calls to backend routes. Then `roam ws context`, `roam ws trace`, etc. work across repos.
+
+**Is Roam compatible with SonarQube / CodeScene?**
+Yes. Roam complements existing tools. Both can run in the same CI pipeline. SARIF output integrates with GitHub Code Scanning.
+
+## Limitations
+
+Static analysis trade-offs:
+
+- **Static analysis primarily** -- can't trace dynamic dispatch, reflection, or eval'd code. Runtime trace ingestion (`roam ingest-trace`) adds production data but requires external trace export
+- **Import resolution is heuristic** -- complex re-exports or conditional imports may not resolve
+- **Limited cross-language edges** -- Salesforce, Protobuf, REST API, and multi-repo edges are supported, but not arbitrary FFI
+- **Tier 2 languages** (Kotlin, Swift, Scala) get basic symbol extraction only
+- **Large monorepos** (100k+ files) may have slow initial indexing
+
+## Troubleshooting
+
+| Problem | Solution |
+|---------|----------|
+| `roam: command not found` | Ensure install location is on PATH. For `uv`: `uv tool update-shell` |
+| `Another indexing process is running` | Delete `.roam/index.lock` and retry |
+| `database is locked` | `roam index --force` to rebuild |
+| Unicode errors on Windows | `chcp 65001` for UTF-8 |
+| Symbol resolves to wrong file | Use `file:symbol` syntax: `roam symbol myfile:MyFunction` |
+| Health score seems wrong | `roam health --json` for factor breakdown |
+| Index stale after `git pull` | `roam index` (incremental). After major refactors: `roam index --force` |
+
+## Update / Uninstall
+
+```bash
+# Update
+pipx upgrade roam-code
+uv tool upgrade roam-code
+pip install --upgrade roam-code
+
+# Uninstall
+pipx uninstall roam-code
+uv tool uninstall roam-code
+pip uninstall roam-code
+```
+
+Delete `.roam/` from your project root to clean up local data.
+
+## Development
+
+```bash
+git clone https://github.com/Cranot/roam-code.git
+cd roam-code
+pip install -e ".[dev]"   # includes pytest, ruff
+pytest tests/              # ~5000 tests, Python 3.9-3.13
+
+# Or use Make targets:
+make dev      # install with dev extras
+make test     # run tests
+make lint     # ruff check
+```
+
+<details>
+<summary><strong>Project structure</strong></summary>
+
+```
+roam-code/
+├── pyproject.toml
+├── action.yml                         # Reusable GitHub Action
+├── src/roam/
+│   ├── __init__.py                    # Version (from pyproject.toml)
+│   ├── cli.py                         # Click CLI (137 commands)
+│   ├── mcp_server.py                  # MCP server (101 tools, 10 resources, 5 prompts)
+│   ├── db/
+│   │   ├── connection.py              # SQLite (WAL, pragmas, batched IN)
+│   │   ├── schema.py                  # Tables, indexes, migrations
+│   │   └── queries.py                 # Named SQL constants
+│   ├── index/
+│   │   ├── indexer.py                 # Orchestrates full pipeline
+│   │   ├── discovery.py               # git ls-files, .gitignore
+│   │   ├── parser.py                  # Tree-sitter parsing
+│   │   ├── symbols.py                 # Symbol + reference extraction
+│   │   ├── relations.py               # Reference resolution -> edges
+│   │   ├── complexity.py              # Cognitive complexity (SonarSource) + Halstead metrics
+│   │   ├── git_stats.py               # Churn, co-change, blame, Renyi entropy
+│   │   ├── incremental.py             # mtime + hash change detection
+│   │   ├── file_roles.py              # Smart file role classifier
+│   │   └── test_conventions.py        # Pluggable test naming adapters
+│   ├── languages/
+│   │   ├── base.py                    # Abstract LanguageExtractor
+│   │   ├── registry.py                # Language detection + aliasing
+│   │   ├── *_lang.py                  # One file per language (19 dedicated + generic)
+│   │   └── generic_lang.py            # Tier 2 fallback
+│   ├── bridges/
+│   │   ├── base.py, registry.py       # Cross-language bridge framework
+│   │   ├── bridge_salesforce.py       # Apex <-> Aura/LWC/Visualforce
+│   │   └── bridge_protobuf.py         # .proto -> Go/Java/Python stubs
+│   ├── catalog/
+│   │   ├── tasks.py                  # Universal algorithm catalog (23 patterns)
+│   │   └── detectors.py              # Anti-pattern detectors with confidence calibration
+│   ├── workspace/
+│   │   ├── config.py                  # .roam-workspace.json
+│   │   ├── db.py                      # Workspace overlay DB
+│   │   ├── api_scanner.py             # REST API endpoint detection
+│   │   └── aggregator.py              # Cross-repo aggregation
+│   ├── graph/
+│   │   ├── builder.py, pagerank.py    # DB -> NetworkX, PageRank
+│   │   ├── cycles.py, clusters.py     # Tarjan SCC, propagation cost, Louvain, modularity Q
+│   │   ├── layers.py, pathfinding.py  # Topo layers, k-shortest paths
+│   │   ├── simulate.py, spectral.py   # Architecture simulation, Fiedler bisection
+│   │   ├── partition.py, fingerprint.py # Multi-agent partitioning, topology fingerprints
+│   │   └── anomaly.py                 # Statistical anomaly detection
+│   ├── commands/
+│   │   ├── resolve.py                 # Shared symbol resolution
+│   │   ├── graph_helpers.py           # Shared graph utilities (adj builders, BFS)
+│   │   ├── context_helpers.py         # Data-gathering helpers for context command
+│   │   ├── gate_presets.py            # Framework-specific gate rules
+│   │   └── cmd_*.py                   # One module per command
+│   ├── analysis/
+│   │   ├── effects.py                 # Side-effect classification engine
+│   │   └── taint.py                   # Taint analysis
+│   ├── refactor/
+│   │   ├── codegen.py                 # Import generation (Python/JS/Go)
+│   │   └── transforms.py             # move/rename/add-call/extract transforms
+│   ├── rules/
+│   │   ├── engine.py                  # YAML rule parser + graph query evaluator
+│   │   ├── builtin.py                 # 10 built-in governance rules
+│   │   ├── ast_match.py               # AST pattern matching with $METAVAR captures
+│   │   └── dataflow.py                # Intra-procedural dataflow analysis
+│   ├── runtime/
+│   │   ├── trace_ingest.py            # OpenTelemetry/Jaeger/Zipkin ingestion
+│   │   └── hotspots.py                # Runtime hotspot analysis
+│   ├── search/
+│   │   ├── tfidf.py                   # TF-IDF semantic search engine
+│   │   ├── index_embeddings.py        # Embedding index builder
+│   │   └── onnx_embeddings.py         # Optional local ONNX semantic backend
+│   ├── security/
+│   │   ├── vuln_store.py              # CVE/vulnerability storage
+│   │   └── vuln_reach.py              # Vulnerability reachability paths
+│   └── output/
+│       ├── formatter.py               # Token-efficient formatting
+│       ├── sarif.py                   # SARIF 2.1.0 output
+│       └── schema_registry.py         # JSON envelope schema versioning
+└── tests/                             # ~5000 tests across 151 test files
+```
+
+</details>
+
+### Dependencies
+
+| Package | Purpose |
+|---------|---------|
+| [click](https://click.palletsprojects.com/) >= 8.0 | CLI framework |
+| [tree-sitter](https://github.com/tree-sitter/py-tree-sitter) >= 0.23 | AST parsing |
+| [tree-sitter-language-pack](https://github.com/nicolo-ribaudo/tree-sitter-language-pack) >= 0.6 | 165+ grammars |
+| [networkx](https://networkx.org/) >= 3.0 | Graph algorithms |
+
+Optional: [fastmcp](https://github.com/jlowin/fastmcp) >= 2.0 (MCP server — install with `pip install "roam-code[mcp]"`)
+
+Optional: Local semantic ONNX stack (`numpy`, `onnxruntime`, `tokenizers`) via `pip install "roam-code[semantic]"`
+
+## Roadmap
+
+### Shipped
+
+- [x] MCP v2 agent surface: in-process execution, compound operations, presets, schemas, annotations, and compatibility profiles.
+- [x] Full command and MCP inventory parity in docs: 137 CLI commands and 101 MCP tools.
+- [x] CI hardening: composite action, changed-only mode, trend-aware gates, sticky PR updater, and SARIF guardrails.
+- [x] Performance foundation: FTS5/BM25 search, O(changed) incremental indexing, DB/index optimizations.
+- [x] Agent governance suite: `vibe-check`, `ai-readiness`, `verify`, `ai-ratio`, `duplicates`, advanced `algo` scoring/SARIF.
+- [x] Ownership/review intelligence: `codeowners`, `drift`, `simulate-departure`, `suggest-reviewers`, `api-changes`, `test-gaps`, `semantic-diff`, `secrets`.
+- [x] Multi-agent operations: `partition`, `affected`, `syntax-check`, workspace-aware context and traces.
+- [x] Budget-aware context delivery: `--budget` (partial rollout), PageRank-weighted truncation, conversation-aware ranking.
+
+### Next
+
+- [x] Terminal demo GIF in README.
+- [ ] GitHub repo topics.
+- [ ] GitHub Discussions enabled.
+- [ ] MCP directory + awesome-list submissions.
+
+## Contributing
+
+```bash
+git clone https://github.com/Cranot/roam-code.git
+cd roam-code
+pip install -e .
+pytest tests/   # all ~5000 tests must pass
+```
+
+Good first contributions: add a [Tier 1 language](src/roam/languages/) (see `go_lang.py` or `php_lang.py` as templates), improve reference resolution, add benchmark repos, extend SARIF converters, add MCP tools.
+
+Please open an issue first to discuss larger changes.
+
+## License
+
+[MIT](LICENSE)