Architecture

Monorepo: CLI/MCP (ontoindex/) + browser UI (ontoindex-web/).

Repository layout

Path	Role
ontoindex/	npm package ontoindex: CLI, MCP server (stdio), HTTP API, ingestion pipeline, LadybugDB graph, embeddings.
ontoindex-web/	Vite + React thin client: graph explorer + AI chat. All queries via ontoindex serve HTTP API.
ontoindex-shared/	Shared TypeScript types and constants (consumed by CLI and Web).
.claude/, ontoindex-claude-plugin/, ontoindex-cursor-integration/	Agent skills and plugin metadata.
eval/	Evaluation harnesses for benchmarking tool usage.
.github/	CI workflows + composite actions (setup-ontoindex/, setup-ontoindex-web/).

End-to-end flow: index → graph → tools

1. Ingestion — analyze.ts → runFullAnalysis (run-analyze.ts) → runPipelineFromRepo (pipeline.ts). DAG of 12 phases builds a KnowledgeGraph in memory, then loads into LadybugDB under .ontoindex/. Repo registered in ~/.ontoindex/registry.json for MCP discovery.

2. Persistence — repo-manager.ts (paths, registry, KuzuDB cleanup). lbug-adapter.ts (graph load, queries, embedding batches).

3. Query layer — three interfaces to the same backend:

   • MCP (stdio): mcp.ts → LocalBackend → tools (tools.ts) + resources (resources.ts)
   • HTTP bridge: serve.ts → Express (api.ts, mcp-http.ts) for web UI
   • CLI direct: ontoindex query|context|impact|cypher in tool.ts

4. Staleness — staleness.ts compares indexed lastCommit to HEAD, surfaces hints.

MCP tools

Tool	Purpose
list_repos	Discover indexed repos
query	Hybrid BM25 + vector search over the graph
cypher	Ad hoc Cypher against the schema
context	Callers, callees, processes for one symbol
impact	Blast radius (upstream/downstream) with risk summary
detect_changes	Map git diffs to affected symbols and processes
rename	Graph-assisted multi-file rename with dry_run preview
api_impact	Pre-change impact report for an API route handler
route_map	API route → handler → consumer mappings
tool_map	MCP/RPC tool definitions and handlers
shape_check	Response shape vs consumer property access mismatches
group_list	List repo groups or details for one group
group_sync	Rebuild group Contract Registry (contracts.json) and bridge graph

query, context, and impact are group-aware: pass repo: "@<groupName>" (or "@<groupName>/<memberPath>" to scope to one member) plus optional service: "<monorepo/path>". Group-mode query merges per-repo results via Reciprocal Rank Fusion; group-mode impact runs the local walk in the chosen member and fans out across boundaries via the Contract Bridge (ontoindex/src/core/group/cross-impact.ts). The previously-planned group_query, group_context, group_impact, group_contracts, group_status MCP tools are intentionally not introduced — group-level state is exposed via resources instead:

Resource URI	Purpose
ontoindex://group/{name}/contracts	Contract Registry (provider/consumer rows + cross-links)
ontoindex://group/{name}/status	Per-member index + Contract Registry staleness

Where to change what

Concern	Start in
CLI commands/flags	src/cli/ (index.ts, per-command modules)
Parsing/graph construction	src/core/ingestion/pipeline-phases/ + pipeline.ts
Graph schema/DB	src/core/lbug/ (schema.ts, lbug-adapter.ts)
MCP tools/resources	src/mcp/server.ts, tools.ts, resources.ts
Cross-repo groups (sync, contracts, @<group> routing)	src/core/group/ (service.ts, cross-impact.ts, sync.ts, bridge-db.ts)
Search ranking	src/core/search/ (BM25, hybrid fusion)
Embeddings	src/core/embeddings/ + src/core/run-analyze.ts
Wiki generation	src/core/wiki/
Language support	src/core/ingestion/languages/ + tree-sitter-queries.ts + ontoindex-shared/src/languages.ts
Import resolution	src/core/ingestion/import-processor.ts + import-resolvers/configs/ + model/resolution-context.ts
Call resolution/MRO	src/core/ingestion/call-processor.ts + model/resolve.ts
Type extraction	src/core/ingestion/type-extractors/
Worker pool	src/core/ingestion/workers/
Web UI	ontoindex-web/src/
CI	.github/workflows/*.yml, .github/actions/

Paths above are relative to ontoindex/ unless they start with ontoindex-web/ or .github/.

---

Pipeline Phase DAG

12 phases defined in ontoindex/src/core/ingestion/pipeline-phases/, each with explicit deps and typed output.

scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
  → crossFile → mro → communities → processes

Phase	File	Deps	Output
scan	scan.ts	(root)	File paths + sizes
structure	structure.ts	scan	File/Folder nodes, CONTAINS edges, allPathSet
markdown	markdown.ts	structure	Section nodes, cross-link edges from .md/.mdx
cobol	cobol.ts	structure	COBOL program/paragraph/section nodes (regex, no tree-sitter)
parse	parse.ts + parse-impl.ts	structure, markdown, cobol	Symbol nodes, IMPORTS/CALLS/EXTENDS edges, extracted routes/tools/ORM queries
routes	routes.ts	parse	Route nodes + HANDLES_ROUTE edges (Next.js, Expo, PHP, decorators)
tools	tools.ts	parse	Tool nodes + HANDLES_TOOL edges
orm	orm.ts	parse	QUERIES edges (Prisma, Supabase)
crossFile	cross-file.ts + cross-file-impl.ts	parse, routes, tools, orm	Cross-file type propagation in topological import order
mro	mro.ts	crossFile, structure	METHOD_OVERRIDES + METHOD_IMPLEMENTS edges
communities	communities.ts	mro, structure	Community nodes + MEMBER_OF edges (Leiden algorithm)
processes	processes.ts	communities, routes, tools, structure	Process nodes + STEP_IN_PROCESS edges

Non-phase files in the same directory: parse-impl.ts, cross-file-impl.ts (implementation), wildcard-synthesis.ts (whole-module import expansion), orm-extraction.ts (sequential ORM fallback), types.ts, runner.ts, index.ts.

DAG runner

runner.ts — static phase graph, no plugins, compile-time type safety.

1. Validation — Kahn's topological sort. Rejects on: duplicate names, missing deps, cycles (DFS traces the concrete cycle path, e.g., A -> B -> C -> A, plus count of transitively blocked dependents).

2. Execution — sequential in topological order. Each phase receives:

   • ctx: PipelineContext — shared mutable KnowledgeGraph, repoPath, progress callback, options
   • deps: ReadonlyMap<string, PhaseResult> — declared deps only (runner filters the results map to prevent hidden coupling)

3. Error handling — wraps phase errors with the phase name, emits terminal error progress event, swallows progress handler errors to preserve the original cause.

4. Timing — per-phase durationMs in PhaseResult, dev-mode console logging.

Design patterns:

• Single graph accumulator — all phases mutate the same KnowledgeGraph in ctx; the graph is the primary output.
• Typed phase access — getPhaseOutput<T>(deps, 'name') for type-safe upstream results.
• Binding accumulator lifecycle — created in parse, disposed by crossFile (in finally). No other phase should take ownership.
• Skippable phases — skipGraphPhases omits MRO/communities/processes (faster tests). skipWorkers forces sequential parsing.

How to add a new phase

1. Create pipeline-phases/my-phase.ts with a PipelinePhase<MyOutput> (name, deps, execute)
2. Export from pipeline-phases/index.ts
3. Add to buildPhaseList() in pipeline.ts

import type { PipelinePhase, PhaseResult } from './types.js';
import { getPhaseOutput } from './types.js';
import type { ParseOutput } from './parse.js';

export interface MyPhaseOutput { /* ... */ }

export const myPhase: PipelinePhase<MyPhaseOutput> = {
  name: 'myPhase',
  deps: ['parse'],
  async execute(ctx, deps) {
    const { allPaths } = getPhaseOutput<ParseOutput>(deps, 'parse');
    // ... write to ctx.graph ...
    return { /* typed output */ };
  },
};

---

Call-Resolution DAG

Typed 6-stage pipeline in call-processor.ts (inside the parse phase) that resolves method/function calls and emits CALLS edges. Language behavior plugs in at two LanguageProvider hook points (stages 3–4); shared code names no languages. Scope: call resolution only — import resolution, type extraction, heritage, and symbol-table population live in other phases.

Stages

extract-call ──▶ classify-form ──▶ infer-receiver ──▶ select-dispatch ──▶ resolve-target ──▶ emit-edge
     (1)              (2)            (3)  [hook]       (4)  [hook]         (5)                 (6)

Stage	Produces	Location
extract-call	ExtractedCallSite (name, form, receiver, argCount)	call-extractors/ (per-language); runs in worker
classify-form	callForm (free/member/constructor) + arity	call-analysis.ts → inferCallForm; shared, runs in worker
infer-receiver	ReceiverEnriched (receiver type finalized)	call-processor.ts; shared default chain, then inferImplicitReceiver hook
select-dispatch	DispatchDecision (primary, fallback, ancestryView)	selectDispatch hook, falls back to shared default
resolve-target	TieredCandidates	model/resolve.ts → lookupMethodByOwnerWithMRO (MRO walk)
emit-edge	CALLS edge in graph	call-processor.ts; writes edge with confidence tier

Provider hooks

Both hooks are optional on LanguageProvider. Ruby is the only current implementer.

inferImplicitReceiver — called after shared infer-receiver defaults. Returns ImplicitReceiverOverride | null.

Inputs	calledName, callForm, receiverName, receiverTypeName, callNode (AST), filePath
Non-null fields	callForm, receiverName, receiverTypeName (required); receiverSource: 'implicit-self' (fixed); hint? (opaque, passed to selectDispatch)
Null	Keep existing ReceiverEnriched state

selectDispatch — called after infer-receiver (including hook). Returns DispatchDecision | null; null uses shared default (constructor → primary:'constructor'; typed receiver → primary:'owner-scoped'; else → primary:'free').

Inputs	calledName, callForm, receiverName, receiverTypeName, receiverSource, hint
Non-null fields	primary: 'owner-scoped' | 'free' | 'constructor'; fallback?: 'free-arity-narrowed'; ancestryView?: 'instance' | 'singleton'; hint?

DispatchDecision field semantics:

• primary: 'owner-scoped' — MRO walk from receiver's type; used when receiver type is known.
• fallback: 'free-arity-narrowed' — after owner-scoped miss, search free-call candidates by arity only (Ruby uses this for implicit-self calls that miss their owner's MRO).
• ancestryView: 'singleton' — walk singleton/class ancestry instead of instance ancestry (Ruby def self.foo bodies, so extend-ed methods are found).

Adding language behavior

1. Implicit receivers — implement inferImplicitReceiver: return null if call already has a receiver; otherwise use findEnclosingClassInfo (ast-helpers.ts) to find the enclosing context, return ImplicitReceiverOverride with receiverSource: 'implicit-self', and optionally set hint for selectDispatch.
2. Custom dispatch — implement selectDispatch: inspect receiverSource and hint, return DispatchDecision with primary, optional fallback, optional ancestryView; return null to keep shared defaults.
3. MRO strategy — confirm mroStrategy is 'first-wins', 'c3', 'ruby-mixin', or 'none'; consumed by lookupMethodByOwnerWithMRO.

Ruby example (languages/ruby.ts + utils/ruby-self-call.ts): inferImplicitReceiver rewrites bare-identifier calls to self.method and sets hint to 'instance'/'singleton'; selectDispatch uses hint for ancestryView and adds fallback: 'free-arity-narrowed' for implicit-self calls.

Code references

Module	Purpose
core/ingestion/call-types.ts	DAG types: ReceiverEnriched, DispatchDecision, ImplicitReceiverOverride
core/ingestion/language-provider.ts	Hook signatures: inferImplicitReceiver, selectDispatch
core/ingestion/call-processor.ts	processCalls: stages 3–6
core/ingestion/model/resolve.ts	lookupMethodByOwnerWithMRO: stage 5 MRO walk
core/ingestion/languages/ruby.ts	Both hooks + mroStrategy: 'ruby-mixin'
core/ingestion/utils/ruby-self-call.ts	Bare-call rewrite for inferImplicitReceiver

---

Language-agnostic graph feeding

16 languages → single unified graph. Four abstraction layers:

 Unified Graph Schema (44 node types, 21 relationship types)
           ↑
 Unified Resolution (3-tier name lookup + MRO walk)
           ↑
 Language Providers (import semantics, type config, export checker, MRO strategy)
           ↑
 Tree-Sitter Queries (per-language S-expressions, unified capture tags)

Language providers

Each language implements LanguageProvider (language-provider.ts). Key fields:

Field	Purpose
id, extensions	Language identity and file matching
treeSitterQueries	S-expression queries for AST extraction
importSemantics	named / wildcard-leaf / wildcard-transitive / namespace
importResolver	Language-specific path → file resolution
exportChecker	Public/exported symbol detection
typeConfig	Type annotation extraction rules
mroStrategy	first-wins / c3 / none

16 providers in languages/index.ts via satisfies Record<SupportedLanguages, LanguageProvider> — missing a language is a compile error.

Unified capture tags

Per-language tree-sitter queries use different AST node names but produce the same semantic capture tags: @definition.class, @definition.function, @call.name, @import.source, @heritage.extends. Downstream extraction needs no language branching. Defined in tree-sitter-queries.ts.

Import resolution

Per-language import resolution uses the configs + factory pattern (like call/method/class extractors). Each language declares an ImportResolutionConfig in import-resolvers/configs/, listing an ordered chain of ImportResolverStrategy functions. createImportResolver() (in resolver-factory.ts) composes them: first non-null result wins. Low-level helpers shared across strategies live alongside the configs in import-resolvers/ (e.g. go.ts, rust.ts, python.ts).

Unified 3-tier algorithm (model/resolution-context.ts), per-language importSemantics controls which tier activates:

Tier	Confidence	Mechanism
1 — same-file	0.95	Symbol table for caller's file
2 — import-scoped	0.9	NamedImportMap chains (named) or all files in importMap (wildcard)
3 — global	0.5	O(1) index lookups: class, impl, callable. Fallback only

Import strategy	Languages	Behavior
named	TS, JS, Java, C#, Rust, PHP, Kotlin	Only explicitly imported names visible
wildcard-leaf	Go, Ruby, Swift, Dart	Whole-package import, no transitive re-exports
wildcard-transitive	C, C++	#include closure chains through re-exports
namespace	Python	Module aliases resolved at call site

Chunked parse-and-resolve

parse processes files in ~20 MB byte-budget chunks to bound memory. Per chunk:

1. Worker pool dispatches files (or sequential fallback via skipWorkers)
2. Each worker: detect language → load grammar → run queries → return unified ParseWorkerResult
3. Synthesize wildcard bindings (wildcard-synthesis.ts)
4. Resolve imports and heritage
5. Collect BindingAccumulator entries for cross-file propagation

Workers: workers/worker-pool.ts, workers/parse-worker.ts.

Heritage and MRO

All languages emit unified ExtractedHeritage (child, parent, EXTENDS/IMPLEMENTS). MRO phase walks the heritage graph using per-language strategy:

• first-wins — Java, C#, C++, TS, Ruby, Go
• c3 — Python (C3 linearization)
• none — single-inheritance languages

Unified walk: lookupMethodByOwnerWithMRO() in model/resolve.ts.

---

Full analysis flow

runFullAnalysis in run-analyze.ts orchestrates everything around the pipeline:

CLI (analyze.ts) → runFullAnalysis(repoPath, options, callbacks)
  1. Early exit if lastCommit == HEAD (unless --force)     [0%]
  2. Cache existing embeddings from prior index             [0%]
  3. runPipelineFromRepo() → KnowledgeGraph                [0-60%]
  4. Clean up legacy KuzuDB files                          [60%]
  5. initLbug() → loadGraphToLbug() via CSV streaming      [60-85%]
  6. Create FTS indexes (File, Function, Class, Method...) [85-90%]
  7. Restore cached embeddings (batch insert)              [88%]
  8. Generate new embeddings if --embeddings               [90-98%]
  9. Save metadata + register repo + update .gitignore     [98-100%]
 10. Generate AI context files (AGENTS.md, CLAUDE.md)      [100%]

Options: --force (rebuild regardless), --embeddings (opt-in, skipped if >50k nodes), --skipGit, --noStats.

Storage

<repo>/.ontoindex/
  ├── lbug           # LadybugDB database
  ├── lbug.wal       # Write-ahead log
  ├── lbug.lock      # Single-writer lock
  └── meta.json      # lastCommit, indexedAt, stats

~/.ontoindex/
  └── registry.json  # Global repo registry (MCP discovery)

Managed by repo-manager.ts.

LadybugDB schema

Defined in lbug/schema.ts. Separate node tables per type, single CodeRelation table.

Node tables: File, Folder, Function, Class, Interface, Method, Constructor, CodeElement, Struct, Enum, Macro, Typedef, Union, Namespace, Trait, Impl, TypeAlias, Const, Static, Property, Record, Delegate, Annotation, Template, Module, Community, Process, Route, Tool, Section, Embedding.

Relation types (CodeRelation.type): CONTAINS, DEFINES, CALLS, IMPORTS, EXTENDS, IMPLEMENTS, HAS_METHOD, HAS_PROPERTY, ACCESSES, METHOD_OVERRIDES, METHOD_IMPLEMENTS, MEMBER_OF, STEP_IN_PROCESS, HANDLES_ROUTE, FETCHES, HANDLES_TOOL, ENTRY_POINT_OF.

Embeddings and search

Embeddings (src/core/embeddings/): Snowflake arctic-embed-xs (384D). Embeddable: File, Function, Class, Method, Interface. Incremental via SHA1 content hash. Separate Embedding table.

Search (src/core/search/): Hybrid BM25 + semantic vector, merged via Reciprocal Rank Fusion (K=60).

Known limitations

Overloaded method resolution

Node IDs use arity suffix (#<paramCount>): Method:file:Class.method#1 vs #2.

Same-arity disambiguation: type-hash suffix ~type1,type2 when collision detected and type annotations present. Languages without types (Python, Ruby, JS) use arity-only. TS/JS overload signatures excluded (collapse to implementation body). See #651.

C++ const-qualified: $const suffix after type-hash when non-const collision exists: Method:file:Container.begin#0$const.

Generic/template types: type-hash uses rawType (full AST text including generics): ~vector<int> vs ~vector<std::string>.

ID stability: collision-only tags mean IDs change when overloads are added. save#1 becomes save#1~int when save(String) is added.

Variadic matching: confidence 0.7 when one side is variadic and the other has fixed count.

METHOD_IMPLEMENTS confidence tiering:

Match quality	Confidence
Exact parameter types match	1.0
Arity match, types unavailable	1.0
Variadic vs fixed	0.7
Insufficient info	0.7

Related docs

• MIGRATION.md — breaking changes and migration guidance
• RUNBOOK.md — operational commands and recovery
• GUARDRAILS.md — safety boundaries for humans and agents
• TESTING.md — how to run tests
• docs/adr/0000-index.md — Architecture Decision Records: per-decision algorithm/technique protocols (worker pool, ensemble, CE rerank, citations, gitMining, embedding pipeline, JobManager, summary mode, COPY fallback, stdout silencing, skeleton-first, intent classifier, LSP bridge)
• AGENTS.md / CLAUDE.md — agent workflows and tool usage