Replace broken TODO-to-issue sync with GitHub-native project management

.github/ISSUE_TEMPLATE/bug.yml

@@ -0,0 +1,71 @@
+name: "🐛 Bug Report"
+description: Report a bug in CORTEX
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting a bug. Please fill in the details below.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: A clear and concise description of the bug.
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Steps to Reproduce
+      description: Minimal steps to reproduce the behavior.
+      placeholder: |
+        1. Call `ingestText(...)` with ...
+        2. Then call `query(...)` with ...
+        3. Observe ...
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+      description: What you expected to happen.
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual Behavior
+      description: What actually happened. Include error messages or screenshots if applicable.
+    validations:
+      required: true
+
+  - type: dropdown
+    id: layer
+    attributes:
+      label: Affected Layer
+      description: Which CORTEX layer does this bug affect?
+      multiple: true
+      options:
+        - Foundation (core/)
+        - Storage (storage/)
+        - Vector Compute (root backends)
+        - Embeddings (embeddings/)
+        - Hippocampus (hippocampus/)
+        - Cortex (cortex/)
+        - Daydreamer
+        - Runtime Harness (runtime/)
+        - CI / Build
+        - Documentation
+    validations:
+      required: true
+
+  - type: input
+    id: browser
+    attributes:
+      label: Browser / Runtime
+      description: Browser version, Electron version, or Node/Bun version.
+      placeholder: "Chrome 120, Electron 28, Bun 1.3.10"

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: "📖 Architecture Reference"
+    url: https://github.com/devlux76/cortex/blob/main/DESIGN.md
+    about: Review DESIGN.md before proposing architectural changes.

.github/ISSUE_TEMPLATE/feature.yml

@@ -0,0 +1,60 @@
+name: "✨ Feature Request"
+description: Propose a new feature or enhancement for CORTEX
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Describe the feature you'd like to see in CORTEX.
+
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: A concise description of the proposed feature.
+    validations:
+      required: true
+
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: Why is this feature needed? What problem does it solve?
+    validations:
+      required: true
+
+  - type: textarea
+    id: design
+    attributes:
+      label: Proposed Design
+      description: How should this feature work? Reference DESIGN.md sections if applicable.
+
+  - type: dropdown
+    id: layer
+    attributes:
+      label: Target Layer
+      description: Which CORTEX layer would this feature primarily affect?
+      multiple: true
+      options:
+        - Foundation (core/)
+        - Storage (storage/)
+        - Vector Compute (root backends)
+        - Embeddings (embeddings/)
+        - Hippocampus (hippocampus/)
+        - Cortex (cortex/)
+        - Daydreamer
+        - Runtime Harness (runtime/)
+        - CI / Build
+        - Documentation
+    validations:
+      required: true
+
+  - type: textarea
+    id: exit-criteria
+    attributes:
+      label: Exit Criteria
+      description: What must be true for this feature to be considered complete?
+      placeholder: |
+        - [ ] Unit tests pass
+        - [ ] Integration test covers end-to-end flow
+        - [ ] DESIGN.md updated if architecture changed

.github/ISSUE_TEMPLATE/task.yml

@@ -0,0 +1,77 @@
+name: "🔧 Implementation Task"
+description: Define a specific implementation task
+labels: ["task"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Define a concrete implementation task. Reference DESIGN.md for architectural context.
+
+  - type: textarea
+    id: objective
+    attributes:
+      label: Objective
+      description: What needs to be built or changed?
+    validations:
+      required: true
+
+  - type: dropdown
+    id: priority
+    attributes:
+      label: Priority
+      options:
+        - "P0: critical — blocks dependent work"
+        - "P1: high — targets next milestone"
+        - "P2: medium — important but not blocking"
+        - "P3: low — polish or nice-to-have"
+    validations:
+      required: true
+
+  - type: dropdown
+    id: layer
+    attributes:
+      label: Target Layer
+      description: Which CORTEX layer does this task target?
+      multiple: true
+      options:
+        - Foundation (core/)
+        - Storage (storage/)
+        - Vector Compute (root backends)
+        - Embeddings (embeddings/)
+        - Hippocampus (hippocampus/)
+        - Cortex (cortex/)
+        - Daydreamer
+        - Runtime Harness (runtime/)
+        - CI / Build
+        - Documentation
+    validations:
+      required: true
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Files to Create or Modify
+      description: List the files this task will touch.
+      placeholder: |
+        - `cortex/MetroidBuilder.ts` (create)
+        - `tests/cortex/MetroidBuilder.test.ts` (create)
+        - `DESIGN.md` (update if architecture changes)
+
+  - type: textarea
+    id: exit-criteria
+    attributes:
+      label: Exit Criteria
+      description: Checklist of conditions that must be met to close this task.
+      placeholder: |
+        - [ ] Implementation complete
+        - [ ] Unit tests passing
+        - [ ] Lint and typecheck clean
+        - [ ] guard:model-derived passes (if numerics changed)
+    validations:
+      required: true
+
+  - type: textarea
+    id: dependencies
+    attributes:
+      label: Dependencies
+      description: List any issues or tasks that must be completed first. Use `#issue_number` references.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,19 @@
+## Summary
+
+<!-- What does this PR do? Reference the issue it addresses with "Closes #123". -->
+
+## Changes
+
+<!-- List the key changes made in this PR. -->
+
+- 
+
+## Checklist
+
+- [ ] Lint passes (`npm run lint`)
+- [ ] Typecheck passes (`npm run build`)
+- [ ] Unit tests pass (`npm run test:unit`)
+- [ ] `guard:model-derived` passes (if numeric constants changed)
+- [ ] DESIGN.md updated (if architecture changed)
+- [ ] No hardcoded model-derived numbers — all sourced from `core/`
+- [ ] No server-side dependencies, cloud calls, or telemetry added

.github/copilot-instructions.md

@@ -18,7 +18,19 @@ The engine models three biological brain regions:
 | `PLAN.md` | Module-by-module implementation status and development phases |
 | `TODO.md` | Prioritized actionable tasks to ship v1.0 |
 
-Keep all documents synchronized with the real code state after every implementation pass.
+Keep `DESIGN.md` synchronized with the real code state after every implementation pass.
+
+## Project Management
+
+All task tracking, prioritization, and status is managed through **GitHub-native features** — not markdown files:
+
+- **GitHub Issues** — Every task, bug, and feature request is a GitHub Issue (use the issue templates in `.github/ISSUE_TEMPLATE/`).
+- **GitHub Projects** — Use project boards for Kanban-style lifecycle tracking (To Do → In Progress → Done).
+- **Milestones** — Group issues by release phase (`v0.1`, `v0.5`, `v1.0`).
+- **Labels** — Auto-applied on PRs by `.github/workflows/auto-label.yml` using path-based rules in `.github/labeler.yml`. Priority labels (`P0`–`P3`) and layer labels (`layer: foundation`, `layer: cortex`, etc.) are used for classification.
+- **Issue linking** — Reference dependencies with `#issue_number`. Use `Closes #N` in PR descriptions to auto-close issues on merge.
+
+Agents with `gh` CLI access can create, update, and close issues directly. Do not create markdown files for task tracking.
 
 ## Directory Structure
 
@@ -119,8 +131,10 @@ Run `npm run guard:model-derived` after any numeric change to verify compliance.
 
 - All CI checks must pass: `lint`, `build` (typecheck), `test:unit`.
 - `npm run guard:model-derived` must pass for any change that touches numeric constants.
-- Keep `README.md`, `CORTEX-DESIGN-PLAN-TODO.md`, and `PROJECT-EXECUTION-PLAN.md` synchronized with any implementation state changes.
-- Record blockers with file path, failure symptom, and next action.
+- PRs are auto-labeled by layer based on changed files (`.github/labeler.yml`).
+- Use the PR template (`.github/PULL_REQUEST_TEMPLATE.md`) — it is pre-populated on every PR.
+- Reference the issue being addressed with `Closes #N` in the PR description.
+- Keep `DESIGN.md` synchronized with any architectural changes.
 
 ## What NOT to Do
 

.github/labeler.yml

@@ -0,0 +1,60 @@
+# Maps file-path globs to labels applied automatically on PRs.
+# Used by the auto-label.yml workflow (actions/labeler).
+
+"layer: foundation":
+  - changed-files:
+      - any-glob-to-any-file: "core/**"
+
+"layer: storage":
+  - changed-files:
+      - any-glob-to-any-file: "storage/**"
+
+"layer: compute":
+  - changed-files:
+      - any-glob-to-any-file:
+          - "VectorBackend.ts"
+          - "WebGPUVectorBackend.ts"
+          - "WebGLVectorBackend.ts"
+          - "WebNNVectorBackend.ts"
+          - "WasmVectorBackend.ts"
+          - "CreateVectorBackend.ts"
+          - "BackendKind.ts"
+          - "TopK.ts"
+          - "Vectors.glsl"
+          - "Vectors.wgsl"
+          - "Vectors.wat"
+
+"layer: embeddings":
+  - changed-files:
+      - any-glob-to-any-file: "embeddings/**"
+
+"layer: hippocampus":
+  - changed-files:
+      - any-glob-to-any-file: "hippocampus/**"
+
+"layer: cortex":
+  - changed-files:
+      - any-glob-to-any-file: "cortex/**"
+
+"layer: daydreamer":
+  - changed-files:
+      - any-glob-to-any-file: "daydreamer/**"
+
+"layer: testing":
+  - changed-files:
+      - any-glob-to-any-file: "tests/**"
+
+"layer: ci":
+  - changed-files:
+      - any-glob-to-any-file:
+          - ".github/workflows/**"
+          - ".github/labeler.yml"
+
+"layer: documentation":
+  - changed-files:
+      - any-glob-to-any-file:
+          - "*.md"
+          - "docs/**"
+          - ".github/copilot-instructions.md"
+          - ".github/ISSUE_TEMPLATE/**"
+          - ".github/PULL_REQUEST_TEMPLATE.md"

.github/workflows/auto-label.yml

@@ -0,0 +1,19 @@
+name: Auto-Label PRs
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Label PR by changed files
+        uses: actions/labeler@v5
+        with:
+          configuration-path: .github/labeler.yml
+          sync-labels: true