cognitive-core 0.2.5 → 0.3.1

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Alex Ngai
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -10,7 +10,7 @@ A TypeScript learning system for AI agents. Records how agents solve problems, e
 - [How It Works](#how-it-works)
 - [Knowledge Bank](#knowledge-bank)
 - [Learning Pipeline](#learning-pipeline)
-- [Three-Speed Pipeline Detail](#three-speed-learning-pipeline)
+- [Learning Pipeline Detail](#learning-pipeline-detail)
 - [CLI](#cli)
 - [Agent Backends](#agent-backends)
 - [Skill Library](#skill-library)
@@ -31,11 +31,11 @@ cognitive-core gives agents persistent, structured memory:
 1. **Trajectories** record what the agent did (ReAct-style thought/action/observation steps)
 2. **Playbooks** distill trajectories into reusable guidance (strategy, tactics, verification criteria)
 3. **Knowledge Bank** extracts and organizes factual knowledge — what agents learn about tools, libraries, and patterns
-4. **Routing** matches incoming tasks to relevant playbooks before the agent starts working, using a learned MoE gating function
+4. **Routing** matches incoming tasks to relevant playbooks before the agent starts working
 5. **Meta-learning** tracks which playbooks helped and adjusts routing over time
-6. **Three-speed learning** — immediate per-trajectory updates (<200ms), energy-triggered batch extraction, and circadian-gated maintenance — all managed by a single `UnifiedLearningPipeline`
+6. **Decoupled learning** — cheap per-trajectory capture on the hot path (<200ms), with consolidation deferred to an offline "dream" that drains a durable queue, plus circadian-gated maintenance — all managed by a single `UnifiedLearningPipeline`
 7. **Temporal compression** — experiences flow through Hot/Warm/Cold/Evicted tiers based on access frequency, keeping memory bounded
-8. **Unified persistence** — all system state lives in a single SQLite database with WAL mode, including learned MoE routing weights, experience clusters, and playbook version history that survive restarts
+8. **Markdown-first persistence** — stable playbook content is canonical in `SKILL.md` files; operational indexes and high-churn state live in a single SQLite database (WAL mode) that is rebuildable from the files
 
 The result: agents that get measurably better at recurring problem types without fine-tuning or prompt engineering.
 
@@ -106,8 +106,8 @@ const trajectory = createTrajectory({
 
 const result = await atlas.processTrajectory(trajectory);
 // result.instantLoop.experienceId  — stored experience
-// result.batchTriggered             — whether batch learning was auto-triggered
-// result.maintenanceTriggered       — whether maintenance cycle ran
+// The trajectory is also durably enqueued for offline consolidation;
+// run `atlas.dream()` (or the `cogcore dream` CLI) to consolidate.
 
 await atlas.close();
 ```
@@ -135,15 +135,13 @@ Every call to `atlas.solve(task)` runs through this pipeline:
 
 ```mermaid
 flowchart TD
-    Task[Task arrives] --> Router[TaskRouter + MoEGate]
+    Task[Task arrives] --> Router[TaskRouter]
 
     Router -->|queries| Memory[MemorySystem]
     Memory --> Exp[ExperienceMemory]
     Memory --> PB[PlaybookLibrary]
     Memory --> KB[KnowledgeBank]
     Memory --> Meta[MetaMemory]
-    Memory --> RB[ReasoningBank]
-    Memory --> CS[CausalStore]
 
     Router --> Decision{RoutingDecision}
 
@@ -153,130 +151,91 @@ flowchart TD
     Backend -->|returns trajectory| Session[AgentSession]
 
     Session --> Check{Succeeded?}
-    Check -->|Yes| PostExec[Post-execution]
+    Check -->|Yes| PostExec[Inline post-execution]
     Check -->|No| Refine{Retry?}
     Refine -->|Yes, max 3x| Agent
     Refine -->|No| PostExec
 
     PostExec --> Usage[PlaybookUsageInference]
-    PostExec --> MetaReflect[MetaLearner reflection]
-    PostExec --> Effective[EffectivenessTracker annotate]
+    PostExec --> Credit[Playbook outcome credit]
 
-    PostExec --> Pipeline[UnifiedLearningPipeline]
-
-    Pipeline --> Immediate[Speed 1: Immediate]
+    PostExec --> Immediate[InstantLoop — hot path]
     Immediate --> Store[Store experience]
     Immediate --> Bump[Bump playbook confidence]
-    Immediate --> QuickK[Extract knowledge notes]
-    Immediate --> Causal[Extract causal edges]
-    Immediate --> Reflexion[Generate reflexion episode]
-
-    Pipeline --> Energy{EnergyEvaluator}
-    Energy -->|threshold reached| Batch[Speed 2: Batch]
-    Energy -->|below threshold| Done[Done]
-    Batch --> Extract[PlaybookExtractor]
-    Batch --> DeepK[Batch knowledge extraction]
-    Batch --> Compress[TemporalCompressor]
-    Batch --> Cluster[ReasoningBank re-cluster]
-    Batch --> Prune[ExperienceMemory prune]
-
-    Batch --> MaintCheck{Maintenance due?}
-    MaintCheck -->|Yes| Maint[Speed 3: Maintenance]
-    MaintCheck -->|No| Done
-    Maint --> Heal[HealingOrchestrator]
-    Maint --> Defrag[Knowledge defrag]
-    Maint --> MetaStrat[Meta-strategy generation]
-    Maint --> Done
-
-    Done -.->|next task| Router
-```
 
-### Post-execution subsystems
+    Immediate --> Queue[(dream_queue — durable SQLite)]
+    Queue -.->|"dream() — explicit, scheduled, or at close"| Dream[Dream: consolidation]
 
-After every `solve()` call, three subsystems run synchronously on the trajectory before it enters the learning pipeline. These require the `RoutingDecision` and injected playbook context, so they **only run via `solve()`** — not via `processTrajectory()`.
+    Dream --> Extract[PlaybookExtractor]
+    Dream --> DeepK[Knowledge extraction]
+    Dream --> Reflexion[Reflexion episodes]
+    Dream --> Compress[TemporalCompressor]
+    Dream --> MetaReflect[Deferred MetaLearner reflection]
+    Dream --> Effective[Deferred effectiveness annotation]
 
-| Subsystem | What it does |
-|-----------|--------------|
-| **PlaybookUsageInference** | Infers which injected playbooks were actually used by the agent. Records outcomes to SkillLibrary for tier management. |
-| **MetaLearner** | Generates a meta-reflection on routing/retrieval effectiveness. Stores observations and periodically generates meta-strategies. |
-| **EffectivenessTracker** | Annotates the trajectory with which playbooks were surfaced vs. applied and which experiences were retrieved. |
-
-All three use workspace templates (LLM-assisted) when an `AgenticTaskRunner` is set, with heuristic fallback otherwise.
-
-### Three-speed learning pipeline
-
-All learning is managed by the `UnifiedLearningPipeline`, which consolidates InstantLoop, batch extraction, energy-based triggering, maintenance scheduling, and healing into a single orchestrator.
+    Dream --> MaintCheck{Maintenance due?}
+    MaintCheck -->|Yes| Maint[Maintenance tasks]
+    Maint --> Defrag[Knowledge defrag]
+    Maint --> Efficacy[Playbook efficacy audits]
+    Maint --> Mutate[Merge / reflective mutation]
+```
 
-#### Speed 1: Immediate (<200ms, no LLM)
+### Post-execution: inline vs deferred
 
-Fires on **every trajectory**. The InstantLoop performs lightweight, synchronous updates:
+After every `solve()` call, only **PlaybookUsageInference** and playbook outcome credit run inline — usage inference is SkillLibrary-coupled and feeds the synchronous solve result. **MetaLearner reflection** and **effectiveness annotation** are deferred to the dream: `solve()` persists a routing snapshot (strategy, playbook matches, surfaced memory IDs) on the queue row, and the dream replays it.
 
-| Operation | Target |
-|-----------|--------|
-| Store experience | ExperienceMemory |
-| Bump matched playbook confidence | PlaybookLibrary |
-| Extract lightweight knowledge notes | KnowledgeBank |
-| Extract causal edges | CausalStore |
-| Generate reflexion episode | ReflexionMemory |
+| Subsystem | When | What it does |
+|-----------|------|--------------|
+| **PlaybookUsageInference** | Inline (solve only) | Infers which injected playbooks were actually used by the agent. Records outcomes to SkillLibrary for tier management. |
+| **Outcome credit** | Inline (solve only) | Attributes task outcome fractionally across injected playbooks, weighted by retrieval score. |
+| **MetaLearner** | Deferred to dream | Generates a meta-reflection on routing/retrieval effectiveness from the persisted routing snapshot. |
+| **EffectivenessTracker** | Deferred to dream | Annotates the trajectory with which playbooks were surfaced vs. applied and which experiences were retrieved. |
 
-After the instant loop, the trajectory is analyzed (heuristic or workspace template) and accumulated for batch.
+### Learning pipeline detail
 
-#### Speed 2: Batch (energy-triggered)
+All learning is managed by the `UnifiedLearningPipeline`. Learning is **decoupled**: the hot path only captures; consolidation happens offline in a "dream".
 
-Triggered by the `EnergyEvaluator` — not just a count threshold. The evaluator computes an energy score from signals:
+#### Immediate (<200ms, no LLM)
 
-| Signal | Weight | Trigger condition |
-|--------|--------|-------------------|
-| Count threshold | — | `pendingCount >= countThreshold` (default: `minTrajectories`) |
-| Contradiction detected | 0.4 | Coherence checker flagged a conflict |
-| Novel domain | 0.3 | First trajectory in an unseen domain |
-| High error rate | 0.2 | Recent failure rate exceeds 60% |
-| Pattern shift | 0.1 | External signal (e.g., from caller) |
+Fires on **every trajectory**. The InstantLoop performs lightweight, synchronous updates — store the experience (ExperienceMemory) and bump matched playbook confidence/frontier state (PlaybookLibrary). Heavier per-trajectory analytics (knowledge notes, reflexion episodes) are deferred off the hot path and run during the dream. The trajectory is then durably enqueued on the SQLite `dream_queue` table.
 
-Batch triggers when `pendingCount >= countThreshold` **or** `energy >= energyThreshold (0.7)`, subject to a debounce interval (`minIntervalMs`, default: 30s).
+#### Dream (offline consolidation)
 
-When batch runs:
+Consolidation happens **only** via `atlas.dream()` — explicitly, on a schedule, or at close; there is no inline batch trigger. The `ConsolidationCoordinator` decides when a dream is due (pending-count threshold, staleness of the oldest queued row, single-flight + cross-process locking) and drives both the idle scheduler and the explicit API.
 
-1. **Playbook extraction** — extract new playbooks from trajectory clusters, refine existing ones
-2. **Batch knowledge extraction** — richer than instant-loop extraction, covers all accumulated trajectories
-3. **Temporal compression** — promote/demote/evict experiences across Hot/Warm/Cold/Evicted tiers
-4. **Re-clustering** — ReasoningBank rebuilds K-means++ clusters from current experiences
-5. **Pruning** — ExperienceMemory prunes beyond `maxExperiences`
-6. **Meta-learning** — MetaLearner generates routing strategies
+When a dream drains the queue it runs:
 
-After batch completes, accumulated trajectories are cleared and the energy evaluator resets.
+1. **Full trajectory analysis** — credit assignment + error patterns
+2. **Playbook extraction** — extract new playbooks from trajectory clusters, refine existing ones
+3. **Knowledge extraction** — richer than hot-path extraction, plus the deferred instant analytics (knowledge notes, reflexion)
+4. **Deferred routing work** — MetaLearner reflection + effectiveness annotation from persisted routing snapshots
+5. **Temporal compression** — promote/demote/evict experiences across Hot/Warm/Cold/Evicted tiers
+6. **Pruning** — ExperienceMemory prunes beyond `maxExperiences`
 
-#### Speed 3: Maintenance (circadian-gated)
+#### Maintenance (circadian-gated)
 
-Runs after batch when the `MaintenanceScheduler` signals readiness. Three scheduling modes:
+Runs after dreams when the `MaintenanceScheduler` signals readiness. Three scheduling modes:
 
 | Mode | When maintenance runs |
 |------|----------------------|
 | `manual` | Only via explicit `runMaintenance({ force: true })` |
-| `afterNBatches` | After every N batch cycles (e.g., `batchInterval: 2`) |
+| `afterNBatches` | After every N dream cycles (e.g., `batchInterval: 2`) |
 | `periodic` | After a time interval since last maintenance |
 
-Built-in maintenance tasks:
-
-| Task | What it does |
-|------|--------------|
-| **healing-cycle** | `HealingOrchestrator` runs anomaly detectors (PlaybookDriftDetector, MemoryBloatDetector) and applies repair strategies |
-| **knowledge-defrag** | KnowledgeBank merges duplicate/overlapping notes |
-| **meta-strategy-generation** | MetaLearner generates new routing strategies from accumulated observations |
-
-Custom maintenance tasks and anomaly detectors can be registered via `registerMaintenanceTask()` and `addAnomalyDetector()`.
+Built-in maintenance tasks: `knowledge-defrag`, `meta-strategy-generation`, `curation-prune`, `pareto-merge-proposing`, `reflective-mutation`, `playbook-decay-detection`, `playbook-efficacy-audit`, `playbook-lifecycle-review`. Custom tasks can be registered via `registerMaintenanceTask()`.
 
 #### `solve()` vs `processTrajectory()`
 
 | | `atlas.solve(task)` | `atlas.processTrajectory(trajectory)` |
 |---|---|---|
-| **Routing** | Yes — TaskRouter + MoEGate | No |
+| **Routing** | Yes — TaskRouter | No |
 | **Agent execution** | Yes — AgentManager + refinement | No (trajectory provided externally) |
-| **Post-execution** | Yes — UsageInference, MetaLearner, EffectivenessTracker | No (requires routing context) |
-| **Three-speed pipeline** | Yes | Yes |
-| **Returns** | `SolveResult` (trajectory, routing, playbook usage) | `ImmediateResult` (instant loop, energy eval, batch/maintenance results) |
+| **Inline post-execution** | Yes — UsageInference, outcome credit | No (requires routing context) |
+| **Immediate capture + dream enqueue** | Yes | Yes |
+| **Deferred routing work in dream** | Yes (routing snapshot on queue row) | No |
+| **Returns** | `SolveResult` (trajectory, routing, playbook usage) | `ImmediateResult` (instant-loop result) |
 
-Use `solve()` when Atlas owns execution. Use `processTrajectory()` to feed in external trajectories — the full three-speed pipeline still runs, but post-execution subsystems that require routing context are skipped.
+Use `solve()` when Atlas owns execution. Use `processTrajectory()` to feed in external trajectories — capture and consolidation still run, but routing-dependent subsystems are skipped.
 
 ### Playbook lifecycle
 
@@ -304,7 +263,7 @@ stateDiagram-v2
 
 ### Memory architecture
 
-Seven memory stores serve different retrieval patterns:
+Five memory stores serve different retrieval patterns:
 
 ```mermaid
 graph LR
@@ -313,8 +272,6 @@ graph LR
         P[PlaybookLibrary]
         K[KnowledgeBank]
         M[MetaMemory]
-        RB[ReasoningBank]
-        CS[CausalStore]
         RF[ReflexionMemory]
     end
 
@@ -340,25 +297,22 @@ graph LR
     P --> VS
     K --> TS
     K -.-> MM
-    CS --> II
-    CS --> TS
-    RB --> TS
     VS -.-> OAI
     VS -.-> VOY
     VS -.-> HF
 
     subgraph Storage
+        SKMD[SKILL.md files — canonical playbooks]
         SQL[SQLite — cognitive-core.db]
         MD[Markdown + YAML]
         SKILL[SQLite — skills.db]
     end
 
     E --> SQL
-    P --> SQL
+    P --> SKMD
+    P -->|rebuildable index| SQL
     M --> SQL
-    CS --> SQL
     RF --> SQL
-    RB -.->|system_state| SQL
     VS --> SQL
     K --> MD
 ```
@@ -366,11 +320,9 @@ graph LR
 | Store | Purpose | Format |
 |-------|---------|--------|
 | **ExperienceMemory** | Episodic — *what happened* | SQLite |
-| **PlaybookLibrary** | Procedural — *how to do things* | SQLite (with version history) |
+| **PlaybookLibrary** | Procedural — *how to do things* | `SKILL.md` files (canonical) + SQLite index with version history |
 | **KnowledgeBank** | Semantic — *facts, concepts, relationships* | Markdown + YAML frontmatter |
 | **MetaMemory** | Meta-learning — *what worked* | SQLite |
-| **ReasoningBank** | Clustered experience retrieval (K-means++) | SQLite (system_state) |
-| **CausalStore** | Cause-effect relationships | SQLite |
 | **ReflexionMemory** | Structured self-reflections | SQLite |
 
 ### Candidate retrieval
@@ -380,7 +332,7 @@ All memory stores use a shared two-phase retrieval pattern:
 1. **InvertedIndex narrowing** — tokenize the query, find candidate IDs via posting lists (fast, O(query tokens))
 2. **Fallback to full scan** — if the index returns fewer candidates than needed, fall back to the full store or domain partition
 
-This is implemented once in `memory/candidate-retrieval.ts` and shared by ExperienceMemory, PlaybookLibrary, and CausalStore.
+This is implemented once in `memory/candidate-retrieval.ts` and shared by ExperienceMemory and PlaybookLibrary.
 
 ### Search and matching
 
@@ -388,9 +340,9 @@ Memory search uses BM25 text matching by default. For higher-quality retrieval,
 
 Knowledge bank search uses text similarity by default, with optional delegation to [minimem](https://github.com/alexngai/minimem) for hybrid vector + BM25 search when available.
 
-### MoE routing gate
+### Routing
 
-The TaskRouter uses a **Mixture-of-Experts inspired gating function** to select routing strategies. Instead of fixed threshold rules, a learned linear gate computes `softmax(W · features)` over the four strategies (direct, adapt, explore, fallback). Weights are updated online from outcome feedback, with per-domain specialization. Cold start falls back to uniform weights (equivalent to the original threshold logic).
+The `TaskRouter` selects one of four strategies (direct, adapt, explore, fallback) from memory-match quality, meta-learned strategy adjustments, and a cheap structural **task-difficulty signal** (`search/task-difficulty.ts` — instruction length, constraint density, step count, tool diversity). A learned MoE gating variant exists but is quarantined in `src/experimental/` pending a passing ablation arm.
 
 ### Temporal compression
 
@@ -401,7 +353,7 @@ Experiences flow through four tiers based on their access frequency:
 | **Hot** | Full data preserved | accessScore > 0.5 |
 | **Warm** | Key steps only (solutionOutput stripped) | accessScore > 0.2 |
 | **Cold** | Single-paragraph summary | accessScore > 0.05 |
-| **Evicted** | Removed (pattern captured in ReasoningBank) | accessScore < 0.05 |
+| **Evicted** | Removed | accessScore < 0.05 |
 
 Hysteresis prevents oscillation: an experience must stay below a threshold for 2 consecutive compression passes before demotion.
 
@@ -439,17 +391,6 @@ knowledge/
 
 Any agent with filesystem access can browse, grep, and read knowledge directly — no special API required.
 
-### Multi-layer knowledge graph
-
-Relationships between knowledge notes are tracked in a multi-layer graph overlay (inspired by [MAGMA](https://arxiv.org/abs/2601.03236)):
-
-| Layer | Captures | Example |
-|-------|----------|---------|
-| **Semantic** | Conceptual relationships | "Prisma *depends-on* PostgreSQL" |
-| **Temporal** | When knowledge was learned | "Observation A *supersedes* B" |
-| **Causal** | Cause-effect chains | "Upgrading TS 5.4 *broke* enum const exports" |
-| **Entity** | Tool/component interactions | "Next.js *uses* React" |
-
 ### Knowledge lifecycle
 
 ```
@@ -524,7 +465,7 @@ Common analysis patterns are consolidated into shared utilities to avoid duplica
 | `classifyError()` / `classifyErrorType()` | TrajectoryAnalyzer, ReflexionGenerator |
 | `detectRepeatedActions()` | TrajectoryAnalyzer, ReflexionGenerator, MetaLearner |
 | `extractToolNames()` | ReflexionGenerator, MetaLearner |
-| `getCandidates()` | ExperienceMemory, PlaybookLibrary, CausalStore |
+| `getCandidates()` | ExperienceMemory, PlaybookLibrary |
 
 ## CLI
 
@@ -603,12 +544,14 @@ cogcore sessions query --agent "Claude Code" --since 2026-01-01 --limit 10
 
 ### Learning pipeline
 
-Operator controls for the three-speed learning pipeline.
+Operator controls for the learning pipeline. Consolidation is decoupled from capture — run `dream` to drain the durable queue.
 
 ```bash
-cogcore learn stats                    # processed count, pending, batch/maintenance cycles
-cogcore learn batch                    # force batch learning on accumulated trajectories
-cogcore learn maintenance              # force maintenance cycle (defrag, healing, meta-strategies)
+cogcore dream                          # one-shot: drain the dream_queue and consolidate
+cogcore dream --watch --interval 60    # long-running scheduler: dream when cadence is due
+cogcore dream failed                   # inspect dead-letter rows
+cogcore learn stats                    # processed count, pending, dream/maintenance cycles
+cogcore learn maintenance              # force maintenance cycle (defrag, audits, meta-strategies)
 ```
 
 ### Skill library
@@ -740,11 +683,14 @@ const skills = await atlas.getSkillLibrary()?.getSkillsForAgent(task);
 
 ### skill-tree integration
 
-When `skillTree.enabled` is true (default), playbooks are published to a `skill-tree` SQLite database via `SqliteStorageAdapter`, making them available to external consumers.
+Playbooks can be published to a `skill-tree` SQLite database via
+`SqliteStorageAdapter`, making them available to external consumers. This
+published skill-tree store is a derived distribution/index layer.
 
-### Team skill library
-
-For multi-agent systems, the `TeamSkillLibrary` surfaces team-level and role-specific playbooks with ELO-based ranking from team outcome feedback.
+For cognitive-core-owned procedural memory, migrated `.atlas` directories use
+`.atlas/playbooks/<skill>/SKILL.md` as the canonical stable artifact and rebuild
+SQLite indexes from those files. Legacy directories without the filesystem
+manifest still use the SQLite playbook table as before.
 
 ## Session Bank
 
@@ -773,12 +719,14 @@ Available templates:
 | `playbook-extraction` | Extract playbooks from trajectory clusters |
 | `knowledge-extraction` | LLM-assisted knowledge extraction |
 | `usage-inference` | Infer which playbooks were actually used |
-| `meta-reflection` | Generate meta-learning observations |
 | `solution-evaluation` | Evaluate solution quality |
 | `refinement-analysis` | Analyze refinement opportunities |
 | `knowledge-defrag` | Merge overlapping knowledge notes |
-| `team-playbook-extraction` | Extract team-level playbooks |
-| `team-trajectory-analysis` | Analyze multi-agent trajectories |
+| `playbook-conditioning` | Condition playbook guidance on context |
+| `playbook-decay-detection` | Detect stale/decaying playbooks |
+| `playbook-efficacy-audit` | Audit playbook effectiveness |
+| `playbook-lifecycle-review` | Review playbook promotion/retirement |
+| `skill-enrichment` | Enrich imported skills |
 
 Templates can run in heuristic mode (no LLM, pattern matching only) or agentic mode (LLM-assisted, higher quality).
 
@@ -793,7 +741,7 @@ const atlas = createAtlasWithAgents([backend], {
   },
   learning: {
     creditStrategy: 'simple',        // 'simple' | 'contribution'
-    minTrajectories: 10,             // batch learning threshold
+    minTrajectories: 10,             // dream consolidation threshold
     deduplicationThreshold: 0.9,     // prevent duplicate playbooks
   },
   router: {
@@ -817,9 +765,6 @@ const atlas = createAtlasWithAgents([backend], {
       enabled: true,                 // auto-extract from trajectories
       useLlmExtraction: false,       // use heuristic extraction
     },
-    graph: {
-      enabledLayers: ['semantic'],   // semantic | temporal | causal | entity
-    },
     surfacing: {
       maxNotesPerTask: 5,
       maxTokensForKnowledge: 2000,
@@ -920,18 +865,18 @@ cognitive-core draws from several lines of research on agent memory and learning
 - **Voyager** - Ever-growing skill libraries with verification
 - **Claudeception** - Lightweight skill persistence for code agents
 - **[A-MEM](https://arxiv.org/abs/2502.12110)** - Zettelkasten-inspired structured notes with dynamic linking (knowledge note format)
-- **[MAGMA](https://arxiv.org/abs/2601.03236)** - Multi-graph decomposition into semantic, temporal, causal, entity layers (graph overlay design)
+- **[MAGMA](https://arxiv.org/abs/2601.03236)** - Multi-graph decomposition into semantic, temporal, causal, entity layers (inspired the graph-overlay experiment now in `src/experimental/`)
 - **[Zep](https://arxiv.org/pdf/2501.13956)** - Entity extraction, community detection, temporal tracking
 - **[Memory Survey](https://arxiv.org/abs/2512.13564)** - Comprehensive survey and taxonomy of factual/experiential/procedural memory
-- **ruvector** - Inspiration for infrastructure improvements: ReasoningBank (K-means++ clustering), MoE routing gate, CoherenceChecker (sheaf-inspired), TemporalCompressor (tiered memory), InstantLoop (hot-path learning)
+- **ruvector** - Inspiration for infrastructure improvements: CoherenceChecker (sheaf-inspired), TemporalCompressor (tiered memory), InstantLoop (hot-path learning). (The ReasoningBank and MoE-gate experiments it also inspired are quarantined in `src/experimental/` pending ablation evidence.)
 
 ## Limitations
 
 - **No cross-domain transfer**. A playbook learned in the `code` domain won't surface for `testing` tasks even if the underlying pattern is the same. Domain tags are string-matched, not semantically compared.
-- **Cold start**. The system needs ~10 trajectories before batch learning kicks in and playbooks start appearing. The instant loop provides per-trajectory updates immediately, and knowledge extraction works per-trajectory, so some learning is available sooner.
+- **Cold start**. The system needs ~10 trajectories before dream consolidation kicks in and playbooks start appearing. The instant loop provides per-trajectory updates immediately, and knowledge extraction works per-trajectory, so some learning is available sooner.
 - **Text-based matching by default**. BM25 and inverted index candidate narrowing work but miss semantic similarity. Vector search requires configuring an embedding provider and adds latency. Knowledge bank search uses text similarity unless minimem is available.
 - **No trajectory quality filtering**. The system stores all trajectories, including ones from poorly-performing agents. Low-quality trajectories can produce low-quality playbooks and knowledge. The deduplication threshold, confidence model, and temporal compression help, but don't solve the garbage-in problem.
-- **Single-machine storage**. All system-internal data lives in a single SQLite database (`cognitive-core.db` with WAL mode), knowledge notes are Markdown files, and skills use a separate `skills.db`. There's no built-in replication, multi-agent concurrency, or cloud storage.
+- **Single-machine storage**. Operational indexes and high-churn state live in SQLite (`cognitive-core.db` with WAL mode), knowledge notes are Markdown files, migrated procedural playbooks are canonical `SKILL.md` files under `.atlas/playbooks`, and published skills use a separate `skills.db`. There's no built-in replication, multi-agent concurrency, or cloud storage.
 - **Extraction is heuristic by default**. Without an LLM extractor configured, both playbook and knowledge extraction use text pattern matching, which produces lower-quality results. LLM-assisted extraction is available via workspace templates.
 
 ## Contributing

package/dist/agents/mock-provider.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"mock-provider.d.ts","sourceRoot":"","sources":["../../src/agents/mock-provider.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAE1E;;;GAGG;AACH,qBAAa,eAAgB,YAAW,WAAW;IACjD,QAAQ,CAAC,IAAI,UAAU;IAEvB,OAAO,CAAC,SAAS,CAAkC;;IA8CnD;;OAEG;IACH,WAAW,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,IAAI;IAIpD;;OAEG;IACG,QAAQ,CAAC,QAAQ,EAAE,OAAO,EAAE,EAAE,QAAQ,CAAC,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;CAiBnF;AAED;;GAEG;AACH,wBAAgB,kBAAkB,IAAI,eAAe,CAEpD"}

package/dist/agents/mock-provider.js.map

@@ -1 +1 @@
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package/dist/agents/types.d.ts.map

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package/dist/agents/types.js

@@ -15,16 +15,17 @@ export class Agent {
      * Reset the agent state
      */
     reset() {
-        this.conversationHistory = [
-            { role: 'system', content: this.config.systemPrompt },
-        ];
+        this.conversationHistory = [{ role: 'system', content: this.config.systemPrompt }];
     }
     /**
      * Send a message and get a response
      */
     async chat(content, options) {
         this.conversationHistory.push({ role: 'user', content });
-        const response = await this.config.provider.complete(this.conversationHistory, { ...this.config.defaultOptions, ...options });
+        const response = await this.config.provider.complete(this.conversationHistory, {
+            ...this.config.defaultOptions,
+            ...options,
+        });
         this.conversationHistory.push({ role: 'assistant', content: response });
         return response;
     }

package/dist/agents/types.js.map

@@ -1 +1 @@
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