Architecture

Module	What it does
models.py	AtomicTask / AtomicTaskBatch — the task contract
decompose.py	Optional LLM-assisted draft of AtomicTask JSON from a loose spec — same contract enforced, human review still required
planner.py	Dependency-ordered execution planning (Kahn topological sort)
agent.py	The agentic session loop (TOOL / RUN / PATCH / SUBMIT grammar, or real function-calling)
llm.py	ChatLLM protocol + OpenAICompatLLM + provider resolution
tools.py	ToolBackend protocol + LocalToolBackend + GraphToolBackend (+ statement_graph; bring your own richer backend)
codegraph.py	Persisted SQLite call graph — symbols, edges, and statement-level def-use tables, incrementally rebuilt
graph_statements.py	Statement-level def-use extraction (Statement-Level-Graph)
symbols.py	The dependency-free symbol index behind LocalToolBackend and codegraph.py's parsing
patch.py	The one canonical SEARCH/REPLACE parser
generator.py / generate_agent.py	Prompt building + the agentic/batch generation pipeline (including the direct multi-file-in-one-completion fast path for independent, dependency-free tasks)
qa.py	Synthesizes a test file per test_triad, gap-filling coverage
repair_agent.py / repair.py	The repair loop: signals → localize → sample → select → gate (Repair-Loop)
bootstrap.py	R16 environment gate + Repo2Run-style agentic fallback (Bootstrap-Gate)
watchdog.py	Production loop: detect a live failure → repair → canary → promote/rollback (Watchdog)
pr.py	Raise a GitHub PR for a landed fix (atomic-forge repair --raise-pr, via gh)
cie_backend.py	Optional CIE-as-MCP-server ToolBackend; required by fix (CIE-Integration)
testgen.py	CIE-grounded regression-test generation + oracle validation (fails-on-buggy gate)
issue.py	Issue URL parsing, gh fetch, shallow clone, install setup for fix
fix.py	atomic-forge fix <url> — one-shot issue → regression test → repair → fork-only PR (Issue-to-PR)
sandbox.py / docker_env.py / stacks.py	Command execution, git, lint gate, test-stack detection (6 ecosystems), optional Docker sandboxing
concurrency.py	The adaptive rate-limit-aware worker pool
checkpoint.py / checkpoint_store.py	Crash-safe, resumable run state (SQLite) (Checkpointing-and-Resumability)
trajectory.py	Append-only JSONL audit trail of every action taken
reporter.py	Write-back protocol for task status/artifacts (bring your own backend)

Protocol extension points (each has at least one real reference implementation): ToolBackend, FailureDetector, DeployTarget, Reporter, RepoStack.