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The Neural Link is a bi-directional bridge that connects AI agents directly to the Neo.mjs runtime. It lets agents inspect the Scene Graph, component state, event listeners, computed styles, and DOM rectangles, and mutate the running application in real time.

Why is Neo.mjs called an Application Engine instead of a framework?

Neo.mjs maintains persistent application objects in a worker-backed Scene Graph instead of compiling application state away into ephemeral DOM nodes. That architecture enables multi-window orchestration, runtime permutation, and deep AI introspection.

What is Context Engineering?

Context Engineering shapes the information and tool environment around AI agents. Neo.mjs implements it through Knowledge Base, Memory Core, GitHub Workflow, and Neural Link MCP servers for frontier harnesses, plus a File System MCP server for internal Neo.ai.Agent local loops.

What is the Neo.mjs Agent OS?

The Neo.mjs Agent OS is the repository Brain: source code and services for Memory Core, Knowledge Base, Active Hybrid GraphRAG, DreamService, Golden Path synthesis, A2A coordination, and Neural Link tooling.

Frontmatter

id	12331
title	Isolate unit-test chroma + sqlite-daemon stores + orphan-purge
state	Closed
labels	bugaitesting
assignees	neo-opus-ada
createdAt	Jun 2, 2026, 1:29 AM
updatedAt	Jun 7, 2026, 7:18 PM
githubUrl	https://github.com/neomjs/neo/issues/12331
author	neo-opus-ada
commentsCount	6
parentIssue	null
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[]
blocking	[x] 10384 Revalidate full-suite Neo.setupClass contamination after test isolation lands, [x] 12180 Orphan test-* Chroma collections accumulate (incomplete test cleanup), [x] 12143 Test runs leak test-* collections into the production unified Chroma store
closedAt	Jun 6, 2026, 1:02 AM

Isolate unit-test chroma + sqlite-daemon stores + orphan-purge

Closed v13.0.0/archive-v13-0-0-chunk-15 bugaitesting

neo-opus-ada commented on Jun 2, 2026, 1:29 AM

Context

Operator-directed (2026-06-02), after exploring the unit-test isolation: the chroma prod-wipe risk is genuinely resolved (process-isolated test-* collection names + afterAll cleanupChromaManager + the FATAL UNIT_TEST_MODE guard protect the real collections), but the orphan accumulation is not. Empirical, live store 2026-06-02:

Chroma: 1,281 test-* orphan collections in default_tenant/default_database vs only 4 real (neo-agent-memory, neo-agent-sessions, neo-knowledge-base, neo-native-graph) — up from #12180's 1,263 (2026-05-29).
SQLite-daemon: test/playwright/unit/ai/daemons/bridge/daemon.spec.mjs writes its db and daemon dir into the prod data dir (DB_PATH = .neo-ai-data/sqlite/test-daemon-${testId}.sqlite, DAEMON_DIR = .neo-ai-data/wake-daemon-test-${testId}) — the SQLite sibling of the chroma leak; 12 leaked dbs were just cleaned but bleed back on every run.

This is the unified test-store-isolation gap that lets #12143/#12180 (and the daemon leak) actually close.

The Problem

Unit tests write to the live stores. Process-isolated names + afterAll cleanup protect prod from wipes and handle the happy path, but interrupted/Ctrl-C/CI-cancel runs and bare-npx bypasses still leak, and there's no ephemeral isolation (so crashes can touch prod-adjacent namespaces) and no purge for the existing backlog. The graph store already does this right (config:112 → :memory: under UNIT_TEST_MODE); chroma + the daemon db do not.

The Architectural Reality

Chroma names: ai/mcp/server/memory-core/config.template.mjs:119-120 — test-memory-${ts}-${rand} / test-session-… under UNIT_TEST_MODE, but the same default_tenant/default_database as prod.
Chroma client: ai/services/memory-core/managers/ChromaManager.mjs#connect() → chromaConnect({client}) (ai/services/shared/vector/chromaClientPrimitives.mjs); client is injectable; ChromaManager.deleteCollection({name, confirmation}) (+ DestructiveOperationGuard) is the safe delete path.
SQLite-daemon: daemon.spec.mjs DB_PATH/DAEMON_DIR resolve under .neo-ai-data/ (prod). cleanupChromaManager (util.mjs) has the FATAL UNIT_TEST_MODE guard.
Already-correct precedent: graph store :memory: under UNIT_TEST_MODE (config:112).
No purge: defragChromaDB.mjs cleans orphaned segment directories only, NOT the test-* collection entries.

The Fix

Chroma ephemeral isolation — under UNIT_TEST_MODE, route the chroma client to an isolated namespace so test collections never land in default_tenant/default_database. Recommended mechanism: a dedicated test tenant/database (chroma multi-tenancy), whole-namespace-droppable. (Mechanism — tenant/db vs throwaway persist-dir vs in-memory — confirm at implementation against the actual client-creation site; prod path stays default_tenant/default_database.)
SQLite-daemon isolation — daemon.spec.mjs DB_PATH + DAEMON_DIR → os.tmpdir()-based paths + afterEach/afterAll cleanup. Off the prod data dir by construction.
Orphan-purge utility — ai/scripts/maintenance/purgeTestCollections.mjs: lists chroma collections, deletes test-memory-* / test-session-* (via the ChromaManager/guarded delete path; or drops the test tenant/db) + the .neo-ai-data/sqlite/test-daemon-* residue. Runnable on demand (clears the existing 1,281 backlog) and optionally at suite start.

Contract Ledger

Target Surface	Source of Authority	Proposed Behavior	Fallback / Edge Case	Docs	Evidence
Chroma client namespace under `UNIT_TEST_MODE`	`ChromaManager#connect` + `config.template.mjs`	Test client resolves to an isolated tenant/database (or equiv); prod unchanged (`default_tenant`/`default_database`)	If multi-tenancy is unavailable at the client/SDK level, fall back to a throwaway persist-dir or keep `test-*` names + mandatory purge-at-suite-start	`config` JSDoc	Static: prod path asserts `default_*`; test path asserts the isolated namespace
`purgeTestCollections.mjs` (new maintenance surface)	this ticket + `ai/scripts/maintenance/` siblings	Deletes `test-memory-`/`test-session-` collections + `test-daemon-*.sqlite` residue; refuses to touch the 4 real collections	Dry-run flag; never deletes a non-`test-*` name (hard guard)	script JSDoc + `npm run` entry	Unit: given a mixed collection list, only `test-*` deleted; real collections untouched

Acceptance Criteria

AC1 — Under UNIT_TEST_MODE, chroma test collections resolve to a namespace distinct from default_tenant/default_database (statically verifiable); by construction no test run — including crashed/npx-bypassed — can create collections in the prod namespace.
AC2 — daemon.spec.mjs writes its db + daemon dir under os.tmpdir(), not .neo-ai-data/ (statically verifiable); afterEach/afterAll cleanup present.
AC3 — purgeTestCollections.mjs deletes test-* chroma collections + test-daemon-* sqlite residue, with a hard guard that never deletes a non-test-* name; running it against the live store leaves only the 4 real collections (verified by a follow-up count).
AC4 — No prod regression: prod chroma still uses default_tenant/default_database; the prod-wipe guards (DestructiveOperationGuard, FATAL UNIT_TEST_MODE guard) remain intact.
AC5 — On merge + purge-run, #12143 (leak) + #12180 (accumulation) are resolved (the daemon leak too).

Out of Scope

GraphLog CDC-log compaction (#12329 — separate; the transient sync log, not the test stores).
Broader graph/Dream-pipeline hygiene.

Resolves-by-completion: #12143, #12180
Sibling: the daemon.spec.mjs SQLite leak (no standalone ticket; folded here)
Adjacent: #12329 (GraphLog compaction), #10867 (the prod-wipe P0 protection this builds on)

Origin Session ID: da9a6007-1250-4363-8c15-dff69eccb3be Retrieval Hint: "unit-test chroma sqlite-daemon ephemeral isolation orphan purge test-* collections"

tobiu referenced in commit b988f02 - "feat(ai): unit-test daemon store isolation + chroma orphan-purge (#12331) (#12336) on Jun 2, 2026, 2:56 AM

tobiu referenced in commit eccfe22 - "feat(ai): isolate unit-test Chroma into a dedicated database (#12335) (#12397) on Jun 3, 2026, 1:11 AM

tobiu Jun 6, 2026, 1:02 AM

ran it:

tobiasuhlig@819fe61f-83c8-4461-95d7-a3ac14b840ba neo % npm run ai:purge-test-collections -- --apply> neo.mjs@12.1.0 ai:purge-test-collections
> node ./ai/scripts/maintenance/purgeTestCollections.mjs --apply
🧹 Purge test collections — APPLY (destructive)
   🔌 Chroma: localhost:8000
Collection schema deserialization was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
Collection schema deserialization was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
Collection neo-knowledge-base was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
   📚 1302 collections total → 1296 test orphans, 6 retained.
   ✨ Retained: test-where, neo-agent-memory, test-where-in, neo-knowledge-base, neo-agent-sessions, neo-native-graph
🔥 Deleting 1296 test orphans:
   …deleted 100/1296
   …deleted 200/1296
   …deleted 300/1296
   …deleted 400/1296
   …deleted 500/1296
   …deleted 600/1296
   …deleted 700/1296
   …deleted 800/1296
   …deleted 900/1296
   …deleted 1000/1296
   …deleted 1100/1296
   …deleted 1200/1296
🧽 SQLite-daemon residue under /Users/Shared/github/neomjs/neo/.neo-ai-data:
   ✅ none found.
Collection schema deserialization was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
Collection schema deserialization was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
Collection neo-knowledge-base was created with the dummy_embedding_function embedding function. However, the @chroma-core/dummy_embedding_function package is not installed. 'add' and 'query' will fail unless you provide them embeddings directly, or install the @chroma-core/dummy_embedding_function package.
🎉 Purge complete: deleted 1296 collections (0 failed); 6 remain (0 test orphans left).

tobiu closed this issue on Jun 6, 2026, 1:02 AM