M31A Codebase Reference

Authoritative Implementation Index: 567 first-party Rust source files across 42 functional subsystems.

This section provides an exhaustive, verified reference for the entire M31A application codebase located at /home/snigdha/Desktop/M31A/src/. Every module, struct, enum, trait, and function documented here corresponds to tested code in revision 3eddbfd3.

Subsystem Navigation Matrix

Subsystem	Layer	Files	Description	Reference Link
Agent Subsystem	L4 Agents	17	Agent roles, lifecycle, supervisor, runner, adaptive replanning, and delegation	Inspect Modules
Capability Registry & Providers	L2 Capabilities	38	Typed capabilities, health monitoring, provider implementations (fs, git, lsp, terminal, web, etc.)	Inspect Modules
Change Management	L6 Execution	7	Workspace change application, review, provenance, authority, and reconciliation	Inspect Modules
Checkpoint & Crash Recovery	L6/L7 Checkpoints	6	Two-phase durable checkpoint protocol, manifest hashing, crash recovery scanner, and safe resume	Inspect Modules
CLI & Dispatch Layer	L9 CLI / Interface	6	Clap 4 argument hierarchy, output formatters, exit codes, and runtime command dispatch	Inspect Modules
Configuration Engine	L1 Configuration	11	8-tier hierarchical configuration precedence, strict schema validation, canonical defaults, and provenance	Inspect Modules
Context Compiler & Tokenizer	L3 Intelligence	8	Token budgeting, prompt envelope assembly, evidence ranking, and context window compaction	Inspect Modules
Autonomy Controller	L8 Autonomy	8	Execution stage transitions, halting criteria, loop detection, and progress monitoring	Inspect Modules
DAG & Critical Path Method	L5 Planning	7	Directed acyclic task graphs, topological sorting, critical path analysis, and reconciliation	Inspect Modules
Deployment & Channels	L9 Deployment	11	Compile-time channel isolation (production vs development), update feeds, installer, and rollback	Inspect Modules
Autonomous Evaluation Harness	L7 Verification	13	Acceptance test scenarios A through H, scoring, and automated evaluation runner	Inspect Modules
Event Bus & Envelopes	L0/L8 Event Bus	4	Broadcast channels, structured telemetry envelopes, and asynchronous event distribution	Inspect Modules
Git & Worktree Isolation	L2 Git Operations	10	Worktree management, branch naming, isolated attribution, trailers, stash, and hosting	Inspect Modules
Domain Identity Types	L0 Domain Identities	18	Strongly typed domain IDs (ExecutionRunId, TaskId, AgentId, ArtifactId, CheckId, etc.)	Inspect Modules
Initialization & Doctor	L9 Initialization	4	Workspace setup wizard, environment diagnostic probes, and lifecycle bootstrapping	Inspect Modules
Interaction & Slash Commands	L9 Interaction	13	Session parser, user-defined slash commands, approval actions, and mention resolution	Inspect Modules
Kernel Core & Seams	L0 Kernel	16	Core seams, architectural invariants, cancellation tokens, hashes, and memory boundaries	Inspect Modules
Engineering Memory	L3 Intelligence	6	Persistent engineering decisions, architectural assumptions, and historical project memory	Inspect Modules
Model & Provider Layer	L3 Intelligence	16	NVIDIA NIM provider, SSE streaming, model catalog, dynamic discovery, and token usage	Inspect Modules
Persistence & SQLite	L0 Persistence	26	SQLite database pool, schema migrations 001-032, repositories, and artifact store	Inspect Modules
Pipeline Execution	L5/L6 Pipeline	18	End-to-end task pipelines, staging, execution harnesses, and lifecycle transitions	Inspect Modules
Planning & Decomposition	L5 Planning	15	Mission decomposition, strategy generation, plan revision, and candidate DAG creation	Inspect Modules
Platform Abstractions	L1 Platform	17	Cross-platform OS primitives (Linux, macOS, Windows), process control, and path handling	Inspect Modules
Policy Engine & Security Gates	L1 Security	15	Non-bypassable policy evaluation, 4 decisions (Allow/Deny/Ask/Escalate), and approvals	Inspect Modules
Process Supervision	L2 Process	11	Process tree supervisor, PID tracking, spool capture, signal escalation, and timeouts	Inspect Modules
Prompt System	L3 Intelligence	16	Prompt registry, template rendering, versioning, and prompt references	Inspect Modules
Recovery & Replanning	L7 Recovery	5	Differential replanning, failure diagnosis, and automated remediation	Inspect Modules
Release Certification	L9 Release	8	Release manifests, 20-point production evidence matrix, and release certification	Inspect Modules
Repository Intelligence	L2 Repository	13	Code search, symbol extraction, dependency graph, and workspace drift detection	Inspect Modules
Execution Reports	L8 Reporting	6	Structured scorecard generation, telemetry summaries, and execution reports	Inspect Modules
Root Application & Runtime	L0-L9 Composition	6	main.rs, lib.rs, error taxonomy, and authoritative AppRuntime composition root	Inspect Modules
Sandbox & Confinement	L1 Sandbox	13	Filesystem sandboxing, network destination policies, and resource confinement	Inspect Modules
Scheduler & Job Admission	L5 Scheduling	10	Global job worker pool, concurrency limits, and task scheduling	Inspect Modules
Skill System	L2 Skills	6	Modular skill discovery, invocation, and in-task execution guidance	Inspect Modules
Authoritative State Management	L8 State	15	Execution run state, session state, task state, and SQLite projection	Inspect Modules
Domain State Machines	L8 State Machine	9	Strict state transition matrices for missions, tasks, agents, and autonomy modes	Inspect Modules
Storage Layout	L0 Storage	2	Platform storage layout, global vs workspace state isolation, and legacy migrations	Inspect Modules
Telemetry & Spans	L8 Telemetry	7	Distributed tracing spans, metrics recording, and operational observability	Inspect Modules
Model Tools & Catalog	L2 Tools	18	Central catalog of 28 core tools and extended tools (fs, git, qa, repo, web, etc.)	Inspect Modules
Ratatui TUI Cockpit	L9 TUI Cockpit	62	62-file terminal cockpit, read-only projection over SQLite, streaming, and screens	Inspect Modules
Verification & Nyquist Gate	L7 Verification	15	7-tier verification hierarchy, evidence snapshot matching, and completion gate	Inspect Modules
Genesis & Engineering Workflows	L8 Workflow	35	35-file multi-stage genesis workflows, ADR creation, charter, synthesis, and roadmap	Inspect Modules

Total Source Footprint: 567 Rust source files, approximately 230,961 lines of code.

Architectural Layers Summary

Architectural Law: Downward Dependency Discipline

Dependencies flow downward only. A lower layer (e.g., L1 Security) may never import or depend on a higher layer (e.g., L8 Autonomy or L9 CLI). All model proposals pass downward through L5 (DAG), L1 (Policy Gate), before reaching L2 (Side-effect tools) or L0 (Persistence).