Nightly Audit: Ruthless Remediation of Root Structure

.gitignore

@@ -124,3 +124,4 @@ build_extensions/uvai-extensions/ai-integrations/MiniCPM-o/
 build_extensions/uvai-extensions/ai-integrations/youtube-mcp/
 youtube_processed_videos/
 quantomcode_private.pem
+prescient-twin-sa-key.json

AGENTS.md

@@ -1,23 +1,53 @@
-# AGENTS.md
-
-## Mission
-To enable autonomous AI agents to efficiently reason, plan, and execute tasks within this repository, specifically focusing on the integration and orchestration of Model Context Protocol (MCP) servers and Video Intelligence pipelines.
-
-## Scope of "Actionable Room"
-Agents are granted permission and encouraged to:
-1.  **Modify and Expand `mcp-servers/`**: Create new MCP servers, update existing ones, and refactor code to improve modularity and performance.
-2.  **Improve Automation**: Create and edit GitHub Actions workflows (`.github/workflows/`) to add robust testing and verification for new features.
-3.  **Refactor for Clarity**: Improve documentation (READMEs) and code structure to facilitate better "Machine Readability" and "Human Understandability".
-
-## Protocols
-1.  **Verify Before Submit**:
-    - Always run relevant verification scripts or tests before submitting changes.
-    - If no test exists for a new feature, **create one**.
-2.  **CI/CD Alignment**:
-    - Ensure all changes pass existing CI checks.
-    - When adding a new component (like an MCP server), add a corresponding CI workflow to ensure it remains functional.
-3.  **Cross-Platform Compatibility**:
-    - Write code that is compatible with Linux and Windows environments whenever possible (e.g., handling `asyncio` loops correctly).
-4.  **Documentation**:
-    - Update `README.md` files when interface changes occur.
-    - Document limitations (e.g., "Text-only CLI wrapper") clearly.
+# Jules Agent System: Architectural Axioms & Protocol
+
+**Role:** High-Integrity Systems Auditor & First-Principles Engineer
+**Objective:** Maintain a clean, scalable, and logic-driven codebase.
+
+## 1. Architectural Geography (The "Where")
+
+Any code added to this repository MUST inhabit one of the following domains. **Root-level directories are strictly forbidden** without a Request for Comments (RFC).
+
+### ✅ `apps/` (The Runnable)
+*   **Purpose:** End-user applications, services, and deployed agents.
+*   **Examples:** Web dashboards, Mobile apps, Python Agent Runners, Electron apps.
+*   **Rule:** If it runs, it lives here.
+
+### ✅ `packages/` (The Shared - TypeScript/Node)
+*   **Purpose:** Shared libraries, UI components, utilities, and schemas.
+*   **Examples:** `ui-kit`, `logger`, `database-client`.
+*   **Rule:** If it's imported by multiple `apps`, it lives here.
+
+### ✅ `mcp-servers/` (The Protocol)
+*   **Purpose:** Model Context Protocol (MCP) servers and connectors.
+*   **Examples:** `github-mcp`, `grok-server`, `filesystem-mcp`.
+*   **Rule:** If it exposes tools via MCP, it lives here.
+
+### ✅ `shared/` (The Shared - Polyglot/Python)
+*   **Purpose:** Shared libraries that are not strictly Node.js packages.
+*   **Examples:** `shared/libs/python-utils`, `shared/libs/xai-grok-wrapper`.
+*   **Rule:** Python libraries and cross-language assets live here.
+
+### ✅ `infrastructure/` (The Foundation)
+*   **Purpose:** Infrastructure as Code (IaC), Docker configurations, CI/CD pipelines, and Service definitions.
+*   **Examples:** `dataconnect`, `kubernetes`, `terraform`.
+*   **Rule:** If it configures the environment, it lives here.
+
+### ✅ `docs/` (The Knowledge)
+*   **Purpose:** Documentation, architectural decision records (ADRs), and knowledge bases.
+*   **Rule:** If it explains "Why" or "How", it lives here.
+
+---
+
+## 2. Ruthless Remediation Protocol (The "How")
+
+When an Agent encounters a violation of these axioms:
+1.  **Identify:** Flag the file/directory.
+2.  **Interrogate:** Why is it here? (5 Whys).
+3.  **Remediate:** Move it to its correct domain immediately.
+4.  **Fortify:** Update this document or add programmatic checks to prevent recurrence.
+
+## 3. Nightly Audit Checklist
+
+*   [ ] No loose directories in root (except `apps`, `packages`, `mcp-servers`, `shared`, `infrastructure`, `docs`, `config`, `scripts`, `tools`, `tests`).
+*   [ ] All new Python code is either in `apps/` (runnable) or `shared/libs/` (importable).
+*   [ ] All new TypeScript code is in `apps/` or `packages/`.

scripts/generate_catalog.py

@@ -63,13 +63,11 @@ def main() -> None:
 
     # Scan locations
     scan_paths = [
-        "projects/*",
-        "mcp-servers/*",
-        "agents-marketplace",
-        "xai-grok-wrapper",
-        "backend",
         "apps/*",
-        "packages/*"
+        "packages/*",
+        "mcp-servers/*",
+        "shared/libs/*",
+        "infrastructure/*"
     ]
 
     for pattern in scan_paths:

shared/PROJECT_CATALOG.md

@@ -4,36 +4,30 @@ Generated by Autonomous Agent.
 
 | Name | Path | Type | Stack | Description |
 |------|------|------|-------|-------------|
+| desktop-overlay | `apps/desktop-overlay` | Unknown | Node.js |  |
 | firebase-project | `apps/firebase` | Unknown | Node.js (Express ^5.1.0) | Firebase project with comprehensive documentation system |
+| prescient-twin | `apps/prescient-twin` | Unknown | Python (Poetry/PDM) |  |
+| software-on-demand | `apps/software-on-demand` | Unknown | Node.js |  |
 | building-production-ai-infrastructure-platform | `apps/web` | Unknown | Node.js (React ^18, Next.js ^14.2.33, TS ^5) |  |
-| _archive | `mcp-servers/_archive` | MCP Server | Unknown |  |
-| ai_ops_skill_mesh_kit | `mcp-servers/ai_ops_skill_mesh_kit` | MCP Server | Python |  |
-| fetch | `mcp-servers/fetch-mcp` | MCP Server | Node.js (TS ^5.7.2) |  |
-| gcp-vector-db | `mcp-servers/gcp-vector-db` | MCP Server | Node.js (TS ^5.3.3) | MCP server for GCP Vector Search using Cloud SQL and pgvector |
+| database | `infrastructure/database` | Unknown | Python |  |
+| dataconnect | `infrastructure/dataconnect` | Unknown | Unknown |  |
+| k8s | `infrastructure/k8s` | Unknown | Unknown |  |
+| terraform | `infrastructure/terraform` | Unknown | Unknown |  |
 | genkitx-mcp | `mcp-servers/genkit-wrapper` | MCP Server | Node.js (TS ^5.3.0) | A Genkit plugin that provides interoperability between Genkit and Model Context Protocol (MCP). Both client and server use cases are supported. |
 | github-mcp-server | `mcp-servers/github` | MCP Server | Node.js | Local installation of GitHub MCP Server |
-| grok-server | `mcp-servers/grok-server` | MCP Server | Node.js (TS ^5.3.3) / Python | MCP server for Grok AI integration |
 | lib | `mcp-servers/lib` | MCP Server | Python |  |
-| mcp-alexnet | `mcp-servers/mcp-alexnet` | MCP Server | Python |  |
-| mcp-bridge | `mcp-servers/mcp-bridge` | MCP Server | Unknown |  |
 | mcp-profiling | `mcp-servers/mcp-profiling` | MCP Server | Python |  |
-| mcp-web-eval-agent | `mcp-servers/mcp-web-eval-agent` | MCP Server | Python (Poetry/PDM) |  |
 | metacognition-tools | `mcp-servers/metacognition-tools` | MCP Server | Node.js (TS ^5.2.2) | MCP server for metacognition tools including Fermi estimation and Red Team attack |
 | perplexity-server | `mcp-servers/perplexity-mcp` | MCP Server | Node.js (TS ^5.3.3) | alls upon perplexity api while i code to get docs, find apis to integrate, and to check deprecated code to make sure everything works properl |
 | puppeteer-server | `mcp-servers/puppeteer-server` | MCP Server | Node.js / Python |  |
 | python-suite | `mcp-servers/python-suite` | MCP Server | Python |  |
-| @modelcontextprotocol/server-code-assistant | `mcp-servers/server-code-assistant` | MCP Server | Node.js | MCP code-assistant Interface |
-| @modelcontextprotocol/server-communication-hub | `mcp-servers/server-communication-hub` | MCP Server | Node.js | MCP communication-hub Interface |
-| @modelcontextprotocol/server-creative-studio | `mcp-servers/server-creative-studio` | MCP Server | Node.js | MCP creative-studio Interface |
-| @modelcontextprotocol/server-data-analysis | `mcp-servers/server-data-analysis` | MCP Server | Node.js | MCP data-analysis Interface |
-| @modelcontextprotocol/server-knowledge-management | `mcp-servers/server-knowledge-management` | MCP Server | Node.js | MCP knowledge-management Interface |
-| server-npm | `mcp-servers/server-npm` | MCP Server | Unknown |  |
-| @modelcontextprotocol/server-workflow-automation | `mcp-servers/server-workflow-automation` | MCP Server | Node.js | MCP workflow-automation Interface |
 | shared-state | `mcp-servers/shared-state` | MCP Server | Python |  |
-| unified-analytics-server | `mcp-servers/unified-analytics` | MCP Server | Node.js (TS ^4.9.5) |  |
+| unified-analytics-server | `mcp-servers/unified-analytics` | MCP Server | Node.js (TS ^5.3.3) |  |
+| web-eval-agent | `mcp-servers/web-eval-agent` | MCP Server | Python (Poetry/PDM) |  |
 | @repo/ai-gateway | `packages/ai-gateway` | Unknown | Node.js (TS ^5) |  |
 | @repo/config | `packages/config` | Unknown | Node.js (TS ^5) |  |
 | @repo/database | `packages/database` | Unknown | Node.js (TS ^5) |  |
+| @eventrelay/embeddings | `packages/embeddings` | Unknown | Node.js (TS ^5.3.0) | pgvector embeddings and semantic search for EventRelay |
 | @repo/error-handling | `packages/error-handling` | Unknown | Node.js (React ^18, TS ^5) |  |
 | @repo/eslint-config | `packages/eslint-config` | Unknown | Node.js (Next.js 14.2.35) |  |
 | @repo/logger | `packages/logger` | Unknown | Node.js (TS ^5) |  |
@@ -44,6 +38,4 @@ Generated by Autonomous Agent.
 | @repo/ui | `packages/ui` | Unknown | Node.js (TS ^5) |  |
 | @eventrelay/vector-store | `packages/vector-store` | Unknown | Node.js (TS ^5.3.0) |  |
 | @repo/workflows | `packages/workflows` | Unknown | Node.js (TS ^5) |  |
-| netmesh-production | `projects/netmesh-production` | Project | Node.js (React ^19.1.1, TS ^5.9.2) |  |
-| software-on-demand | `projects/software-on-demand` | Project | Node.js |  |
-| xai-grok-wrapper | `xai-grok-wrapper` | Unknown | Python |  |
+| xai-grok-wrapper | `shared/libs/xai-grok-wrapper` | Unknown | Python |  |