memory-journal-mcp 8.0.1 → 9.1.0

package/README.md

@@ -2,78 +2,82 @@
 
 <!-- mcp-name: io.github.neverinfamous/memory-journal-mcp -->
 
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+[![GitHub](https://img.shields.io/badge/GitHub-neverinfamous/memory--journal--mcp-blue?logo=github)](https://github.com/neverinfamous/memory-journal-mcp) [![npm](https://img.shields.io/npm/v/memory-journal-mcp)](https://www.npmjs.com/package/memory-journal-mcp) [![Docker Pulls](https://img.shields.io/docker/pulls/writenotenow/memory-journal-mcp)](https://hub.docker.com/r/writenotenow/memory-journal-mcp)
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+[![MCP Registry](https://img.shields.io/badge/MCP_Registry-Published-green)](https://registry.modelcontextprotocol.io/v0/servers?search=io.github.neverinfamous/memory-journal-mcp) [![Security](https://img.shields.io/badge/Security-Enhanced-green.svg)](SECURITY.md) [![TypeScript](https://img.shields.io/badge/TypeScript-Strict-blue.svg)](https://github.com/neverinfamous/memory-journal-mcp)
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 **[📚 Full Documentation (Wiki)](https://github.com/neverinfamous/memory-journal-mcp/wiki)** • **[Changelog](CHANGELOG.md)** • **[Security](SECURITY.md)** • **[Release Article](https://adamic.tech/articles/memory-journal-mcp-server)**
 
-🎯 **AI Context + Project Intelligence:** Bridge disconnected AI sessions with persistent project memory and **automatic session handoff** — with full GitHub workflow integration.
+> [!TIP]
+> **Value Proposition**
+> Bridge disconnected AI sessions seamlessly. Enable persistent project memory instantly. Automate handoffs with robust GitHub integration. Eliminate AI amnesia today.
 
 **🚀 Quick Deploy:**
 
-- **[npm Package](https://www.npmjs.com/package/memory-journal-mcp)** - `npm install -g memory-journal-mcp`
+- **[npm Package](https://www.npmjs.com/package/memory-journal-mcp)** - `npm install -g memory-journal-mcp` (or `pnpm add -g memory-journal-mcp`)
 - **[Docker Hub](https://hub.docker.com/r/writenotenow/memory-journal-mcp)** - Alpine-based with full semantic search
 
-## 🧠 Stop Experiencing AI Amnesia
+## 🧠 Eliminate AI Amnesia
 
-When managing large projects with AI assistance, you face a critical challenge:
+Large projects face a critical challenge. You lose context between sessions.
 
-- **Thread Amnesia** - Each new AI conversation starts from zero, unaware of previous work.
-- **Lost Context** - Decisions, implementations, and learnings scattered across disconnected threads.
-- **Repeated Work** - AI suggests solutions you've already tried or abandoned.
-- **Context Overload** - Manually copying project history into every new conversation.
+- **Stop Thread Amnesia** - AI conversations start fresh. They ignore previous work.
+- **Retain Deep Context** - Decisions and code scatter across threads; Memory Journal preserves them automatically.
+- **End Repeated Work** - AI repeats failed solutions; persistent history tracks every prior attempt.
+- **Prevent Context Overload** - Manual history copying wastes tokens; dynamic briefings deliver targeted context automatically.
 
-Memory Journal solves this by acting as your project's **long-term memory**, bridging the gap between fragmented AI sessions.
+Memory Journal builds your project's long-term memory. It acts as a **Project Context Graph** for AI-assisted engineering. It bridges **human workflows** (Issues, PRs, Kanban, Milestones) with **agent execution** (Git, tests, decisions).
 
 ---
 
 **Experience true context-aware development:**
 
 - _"Why did we choose SQLite over Postgres for this service last month?"_ (Semantic search)
-- _"Run the `/issue-triage` workflow on the top priority ticket in the Kanban board."_ (GitHub operations)
+- _"Run the `/issue-commander` (`triage` workflow) on the top priority ticket in the Kanban board."_ (GitHub operations)
 - _"Who has been touching the auth module recently, and what's our team collaboration density?"_ (Team analytics)
-- _"I'm stuck on this database error. Raise a 'blocker' flag for @sarah so her agent sees it next session."_ (Hush Protocol)
-- _"Close issue #42 and log an entry explaining our architectural fix for the parsing bug."_ (Context lifecycles)
+- _"Commit the changes and automatically generate a structured journal entry using the \`--journal\` wrapper flag."_ (Automated lifecycles)
 - _"Draw a visual graph showing how my last 10 architectural decisions relate to each other."_ (Knowledge graph)
 
-**[See complete examples & prompts →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Examples)**
+**Comprehensive access to internal state via resources (`memory://briefing`, `memory://workflows`, `memory://rules`, `memory://health`, `memory://help`, `memory://staleness`, GitHub status/milestones, team stats, and metrics/latency). Dynamic repo variants also support cross-repo targeting (like `memory://briefing/{+repo}` or `memory://kanban/{+repo}/{project_number}`).** **[Resources documentation →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Resources)**
 
 ---
 
 ## 🎯 What Sets Us Apart
 
-**73 MCP Tools** · **19 Workflow Prompts** · **46 Resources** · **10 Tool Groups** · **Code Mode** · **GitHub Commander** (Issue Triage, PR Review, Milestone Sprints, Security/Quality/Perf Audits) · **GitHub Integration** (Issues, PRs, Actions, Kanban, Milestones, Insights) · **Team Collaboration** (Shared DB, Vector Search, Cross-Project Insights, Hush Protocol Flags)
-
-| Feature                       | Description                                                                                                                                                                                         |
-| ----------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **Session Intelligence**      | Agents auto-query project history, create entries at checkpoints, and hand off context between sessions via `/session-summary` and `team-session-summary`                                           |
-| **GitHub Integration**        | 18 tools for Issues, PRs, Actions, Kanban, Milestones (%), Copilot Reviews, and 14-day Insights                                                                                                     |
-| **Dynamic Project Routing**   | Seamlessly switch contexts and access CI/Issue tracking across multiple repositories using a single server instance via `PROJECT_REGISTRY`                                                          |
-| **Knowledge Graphs**          | 8 relationship types linking specs → implementations → tests → PRs with Mermaid visualization                                                                                                       |
-| **Hybrid Search**             | Reciprocal Rank Fusion combining FTS5 keywords, semantic vector similarity, auto-heuristics, and date-range filters                                                                                 |
-| **Code Mode**                 | Execute multi-step operations in a trusted-admin execution environment — up to 90% token savings via `mj.*` API                                                                                     |
-| **Adaptive Session Briefing** | `memory://briefing` dynamically adapts to deliver real-time workspace context — including live CI health, local Git status, dynamic path routing, and unreleased changes — in ~350 optimized tokens |
-| **Reports & Analytics**       | Standups, retrospectives, PR summaries, digests, period analyses, and milestone tracking                                                                                                            |
-| **Hush Protocol (Flags)**     | Replace Slack/Teams noise with structured, actionable, and searchable AI flags (blockers, reviews) that automatically surface in session briefings                                                  |
-| **Team Collaboration**        | 28 tools with full parity — CRUD, vector search, relationship graphs, cross-project insights, author attribution, Hush Protocol flags (list, update, reopen, analytics)                             |
-| **Data Interoperability**     | Bidirectional Markdown roundtripping, unified IO namespace, and schema-safe JSON exports with hard bounds-checked path traversal defenses                                                           |
-| **Backup & Restore**          | One-command backup/restore with automated scheduling, retention policies, and safety-net auto-backups                                                                                               |
-| **Auto-Pruning**              | Smart garbage collection based on significance scores to soft-delete low-value entries and maintain vector relevance over long-running projects                                                     |
-| **Security & Transport**      | OAuth 2.1 (RFC 9728/8414, JWT/JWKS, scopes), Streamable HTTP + SSE, rate limiting, CORS, SQL injection prevention, non-root Docker                                                                  |
-| **Structured Error Handling** | Every tool returns `{success, error, code, category, suggestion, recoverable}` — agents get classification, remediation hints, and recoverability signals                                           |
-| **Agent Collaboration**       | IDE agents and Copilot share context; review findings become searchable knowledge; agents suggest reusable rules and skills ([setup](docs/copilot-setup.md))                                        |
-| **Native Agent Skills**       | Bundled foundational coding paradigms (`autonomous-dev`, `python`, `docker`, `tailwind-css`, `golang`, `playwright-standard`, etc.) establishing permanent AI behavior and architecture rules       |
-| **GitHub Commander**          | Pipeline skills for issue triage, PR reviews, sprint milestones, and security/quality/performance audits with journal trails ([docs](skills/github-commander/SKILL.md))                             |
+**MCP Tools** · **Workflow Prompts** · **Resources** · **Tool Groups** · **Code Mode** · **GitHub Commander** (Issue Triage, PR Review, Milestone Sprints, Security/Quality/Perf Audits) · **GitHub Integration** (Issues, PRs, Actions, Kanban, Milestones, Insights) · **Team Collaboration** (Shared DB, Vector Search, Cross-Project Insights)
+
+| Feature                       | Description                                                                                                                                                                                          |
+| ----------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Session Intelligence**      | Auto-query project history, create checkpoints, and hand off context between sessions automatically.                                                                                                 |
+| **GitHub Integration**        | Manage Issues, PRs, Actions, Kanban boards, and milestones. Access Copilot reviews and repository insights.                                                                                          |
+| **Dynamic Project Routing**   | Switch contexts seamlessly and access CI/Issue tracking across multiple repositories from a single server instance.                                                                                  |
+| **Knowledge Graphs**          | Link specifications, implementations, tests, and PRs visually using Mermaid diagrams.                                                                                                                |
+| **Hybrid Search**             | Find entries instantly using a blend of keyword, semantic, and date-range searches.                                                                                                                  |
+| **Code Mode**                 | Execute multi-step operations efficiently in a sandboxed environment to reduce token usage.                                                                                                          |
+| **Adaptive Session Briefing** | Deliver real-time workspace context dynamically, including live CI health, local Git status, and unreleased changes.                                                                                 |
+| **Reports & Analytics**       | Generate standups, retrospectives, PR summaries, digests, and period analyses.                                                                                                                       |
+| **Heuristic Scoring**         | Optimize context delivery by scoring entries based on veracity and impact.                                                                                                                           |
+| **Team Collaboration**        | Share databases across teams with cross-project insights, author attribution, and role-based access control.                                                                                         |
+| **Data Interoperability**     | Export schemas safely, sync Markdown directories, and maintain a unified IO namespace.                                                                                                               |
+| **Backup & Restore**          | Secure data with automated scheduling, retention policies, and one-command restores.                                                                                                                 |
+| **Auto-Pruning**              | Soft-delete low-value entries automatically to maintain search relevance over long-running projects.                                                                                                 |
+| **Security & Transport**      | Ensure secure connections with OAuth 2.1, Streamable HTTP, rate limiting, and SQL injection prevention.                                                                                              |
+| **Structured Error Handling** | Provide agents with classification, remediation hints, and recoverability signals on every tool call.                                                                                                |
+| **Agent Collaboration**       | Share context between IDE agents and Copilot. Search review findings and let agents suggest reusable rules.                                                                                          |
+| **Native Agent Skills**       | Establish permanent AI behavior and architecture rules using bundled foundational coding paradigms.                                                                                                  |
+| **GitHub Commander**          | Audit code, triage issues, review PRs, and run sprint milestones via automated pipeline skills.                                                                                                      |
+
+---
+
+### Isolate Environments with Multi-Tenancy
+
+Memory Journal supports multi-tenancy out of the box via the `workspace_id` construct, acting as a strict isolation barrier for multiple journals sharing the same SQLite database file.
+
+- **Auto-Resolution:** When `workspace_id` is omitted, the server automatically resolves the target workspace. It matches `project_number` against `PROJECT_REGISTRY`, checks content/tag keyword aliases, or inspects `process.cwd()` before falling back to `DEFAULT_WORKSPACE_ID` (default: `default`).
+- **Data Partitioning & Cross-Workspace Queries:** Core CRUD, Soft-Delete/Restore, FTS5 Search, Vector Semantic Search (`semantic_search`), and Analytics tools enforce `workspace_id` isolation end-to-end. Read and search tools accept `workspace_id: "*"` to query across all workspaces. External write and mutation paths reject wildcard overrides.
+- **Immutability & Controlled Migration:** Entries receive a `workspace_id` upon creation that standard updates cannot overwrite directly. To migrate an entry across workspaces, call `update_entry` with `workspace_id: "*"` and `target_workspace_id`.
+- **Server Config:** Set `--default-workspace-id` (or the `DEFAULT_WORKSPACE_ID` environment variable) to configure the default fallback workspace for the server instance. This lets you run multiple isolated journal interfaces on a single physical database.
 
 ---
 
@@ -122,229 +126,129 @@ flowchart TB
 _Suggested Rule (Add to AGENTS.md, GEMINI.md, system prompts, etc.)_
 
 <details>
-<summary><strong>View Mandatory Session Start Routine</strong></summary>
-
-🛑 MANDATORY SESSION START ROUTINE
+<summary><strong>View Session Initialization Routine</strong></summary>
 
-Before addressing the user's first request in a session/thread, complete these steps:
+🛑 Session Initialization Routine
 
-1. Read the briefing using the `read_resource` tool: `memory://briefing/{repo_name}`.
-   - Infer `repo_name` from context of user's prompt. Use `memory://briefing` as fallback only if necessary.
-2. Your first response MUST begin with the entire briefing content. Use this format:
+When the user initializes the session context by executing the `load-briefing` prompt:
 
+1. You will receive the output of the `memory://briefing/{repo_name}` resource.
+2. Prepend your response EXACTLY as:
    > **📋 Briefing loaded** — `{repo_name}`
-   >
-   > _{paste **ENTIRE** briefing here}_ (It isn't always easy for users to access in IDEs)
-
-3. Then address the user's request below the briefing.
-4. Do NOT autonomously resume work on issues mentioned in the briefing.
+   > _{paste ENTIRE briefing here}_
+3. Address the user's request below the briefing.
+4. NEVER autonomously execute tasks listed in the briefing.
+5. Do NOT proactively ask the user to load the briefing. Wait for them to use the prompt.
 </details>
 
 ---
 
-### Tool Filtering
+### Control Access with Tool Filtering
 
 > [!IMPORTANT]
-> All shortcuts and tool groups include **Code Mode** (`mj_execute_code`) by default for token-efficient operations. To exclude it, add `-codemode` to your filter: `--tool-filter starter,-codemode`
-
-Control which tools are exposed via `MEMORY_JOURNAL_MCP_TOOL_FILTER` (or CLI: `--tool-filter`):
-
-| Filter               | Tools | Use Case                 |
-| -------------------- | ----- | ------------------------ |
-| `full`               | 73    | All tools (default)      |
-| `starter`            | ~11   | Core + search + codemode |
-| `essential`          | ~7    | Minimal footprint        |
-| `readonly`           | 17    | Disable all mutations    |
-| `-github`            | 52    | Exclude a group          |
-| `-github,-analytics` | 50    | Exclude multiple groups  |
+> All shortcuts and tool groups always include **Code Mode** (`mj_execute_code`) and **Runtime Configuration** (`update_configuration`) as escape-hatch tools so agents can never lock themselves out of the configuration system or Code Mode.
+
+Control which tools are exposed using any of the 3 configuration sources (precedence: CLI flag > environment variable > config file):
+- **CLI flag**: `--tool-filter <filter>`
+- **Environment variable**: `MEMORY_JOURNAL_MCP_TOOL_FILTER` *(Note: `TOOL_FILTER` is only a fallback display variable in the session briefing and does **not** activate tool filtering on its own)*
+- **`memory-journal.config.{yaml,yml,json}` key**: `"toolFilter"`
+
+| Filter               | Use Case                            |
+| -------------------- | ----------------------------------- |
+| `full`               | All tools (default)                 |
+| `starter`            | Core + search + codemode            |
+| `essential`          | Minimal footprint                   |
+| `readonly`           | Disable all mutations               |
+| `codemode`           | `mj_execute_code` + runtime config  |
+| `-github`            | Exclude a group                     |
+| `-github,-analytics` | Exclude multiple groups             |
 
 **Filter Syntax:** `shortcut` or `group` or `tool_name` (whitelist mode) · `-group` (disable group) · `-tool` (disable tool) · `+tool` (re-enable after group disable)
 
 **Custom Selection:** List individual tool names to create your own whitelist: `--tool-filter "create_entry,search_entries,semantic_search"`
 
-**Groups:** `core`, `search`, `analytics`, `relationships`, `io`, `admin`, `github`, `backup`, `team`, `codemode`
+**Groups:** `core`, `search`, `analytics`, `relationships`, `io`, `admin`, `github`, `git`, `backup`, `team`, `codemode`
 
 **[Complete tool filtering guide →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Tool-Filtering)**
 
 ---
 
-## 📋 Core Capabilities
+## 📋 Unlock Core Capabilities
 
-### 🛠️ **73 MCP Tools** (10 Groups)
+### 🛠️ **MCP Tools**
 
-| Group           | Tools | Description                                                                                                                                                               |
-| --------------- | ----- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `codemode`      | 1     | Code Mode (sandboxed code execution) 🌟 **Recommended**                                                                                                                   |
-| `core`          | 6     | Entry CRUD, tags, test                                                                                                                                                    |
-| `search`        | 4     | Text search, date range, semantic, vector stats                                                                                                                           |
-| `analytics`     | 2     | Statistics, cross-project insights                                                                                                                                        |
-| `relationships` | 2     | Link entries, visualize graphs                                                                                                                                            |
-| `io`            | 3     | JSON/Markdown export and File-level Markdown Data Integration Interoperability (Import/Export)                                                                            |
-| `admin`         | 5     | Update, delete, rebuild/add to vector index, merge tags                                                                                                                   |
-| `github`        | 18    | Issues, PRs, context, Kanban, **Milestones**, **Insights**, **issue lifecycle**, **Copilot Reviews**                                                                      |
-| `backup`        | 4     | Backup, list, restore, cleanup                                                                                                                                            |
-| `team`          | 28    | CRUD, search, stats, relationships, IO (Markdown import/export), backup, vector search, cross-project insights, matrix, **Hush Protocol flags** (requires `TEAM_DB_PATH`) |
+| Group           | Description                                                                                                                                                                                       |
+| --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `codemode`      | Code Mode (sandboxed code execution) 🌟 **Recommended**                                                                                                                                           |
+| `core`          | Entry creation/read/history, tags, resource & briefing helpers, anchor staleness, test                                                                                                            |
+| `search`        | Text search, date range, semantic, vector stats, deleted entries, cross-team                                                                                                                      |
+| `analytics`     | Statistics, cross-project insights                                                                                                                                                                |
+| `relationships` | Link entries, visualize graphs                                                                                                                                                                    |
+| `io`            | JSON/Markdown export, Markdown directory import/export, and external knowledge base import (Notion, Obsidian, Logseq)                                                                              |
+| `admin`         | Update configuration, project registry management, entry update/delete/restore, rebuild/add to vector index, merge tags, search audit log, auto-prune, bulk operations (batch create/update/delete) |
+| `github`        | Issues, PRs, context, Kanban, **Milestones**, **Insights**, **issue lifecycle**, **Copilot Reviews**                                                                                              |
+| `git`           | Commit history, search, release info, patterns, staleness checks                                                                                                                                  |
+| `backup`        | Backup, list, restore, cleanup                                                                                                                                                                    |
+| `team`          | CRUD, search, stats, relationships, IO (Markdown & external import/export), backup, vector search, cross-project insights, matrix, RBAC member management, author aliases (requires `TEAM_DB_PATH`) |
 
 **[Complete tools reference →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Tools)**
 
-### 🎯 **19 Workflow Prompts**
-
-- `find-related` - Discover connected entries via semantic similarity
-- `prepare-standup` - Daily standup summaries
-- `prepare-retro` - Sprint retrospectives
-- `weekly-digest` - Day-by-day weekly summaries
-- `analyze-period` - Deep period analysis with insights
-- `goal-tracker` - Milestone and achievement tracking
-- `get-context-bundle` - Project context with Git/GitHub/Kanban
-- `get-recent-entries` - Formatted recent entries
-- `project-status-summary` - GitHub Project status reports
-- `pr-summary` - Pull request journal activity summary
-- `code-review-prep` - Comprehensive PR review preparation
-- `pr-retrospective` - Completed PR analysis with learnings
-- `actions-failure-digest` - CI/CD failure analysis
-- `project-milestone-tracker` - Milestone progress tracking
-- `confirm-briefing` - Acknowledge session context to user
-- `session-summary` - Create a session summary entry with accomplishments, pending items, and next-session context
-- `team-session-summary` - Create a retrospective team session summary entry securely isolated to the team database
-- `adversarial-plan-review` - Multi-pass adversarial plan review with structured dimensions, scoring rubric, and prior plan context
-- `flag-dashboard` - Triage active flags with priority assessment and resolution guidance
-
-**[Complete prompts guide →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Prompts)**
-
-### 📡 **46 Resources** (29 Static + 17 Template)
-
-**29 Static Resources** (appear in resource lists):
-
-- `memory://briefing` - **Session initialization**: compact context for AI agents (~350 tokens) — includes server version, surface area (tools/resources/prompts), test health, unreleased changes, analytics, `localTime`, and optional `activeFlags`
-- `memory://instructions` - **Behavioral guidance**: complete server instructions for AI agents
-- `memory://recent` - 10 most recent entries
-- `memory://significant` - Significant milestones and breakthroughs
-- `memory://graph/recent` - Live Mermaid diagram of recent relationships
-- `memory://health` - Server health & diagnostics
-- `memory://graph/actions` - CI/CD narrative graph
-- `memory://actions/recent` - Recent workflow runs
-- `memory://tags` - All tags with usage counts
-- `memory://statistics` - Journal statistics
-- `memory://rules` - User rules file content for agent awareness
-- `memory://workflows` - Available agent workflows summary
-- `memory://skills` - Agent skills index (names, paths, excerpts)
-- `memory://github/status` - GitHub repository status overview
-- `memory://github/insights` - Repository stars, forks, and 14-day traffic summary
-- `memory://github/milestones` - Open milestones with completion percentages
-- `memory://team/recent` - Recent team entries with author attribution
-- `memory://team/statistics` - Team entry counts, types, and author breakdown
-- `memory://help` - Tool group index with descriptions and tool counts
-- `memory://metrics/summary` - Aggregate tool call metrics since server start (calls, errors, token estimates, duration) — HIGH priority
-- `memory://metrics/tokens` - Per-tool token usage breakdown sorted by output token cost — MEDIUM priority
-- `memory://metrics/system` - Process-level metrics: memory (MB), uptime (s), Node.js version, platform — MEDIUM priority
-- `memory://metrics/users` - Per-user call counts (populated when OAuth user identifiers are present) — LOW priority
-- `memory://audit` - Last 50 write/admin tool call entries from the JSONL operational telemetry log (requires `AUDIT_LOG_PATH`)
-- `memory://flags` - Active (unresolved) team flags dashboard (requires `TEAM_DB_PATH`)
-- `memory://flags/vocabulary` - Configured flag vocabulary terms
-- `memory://flags/history` - Recently resolved flags with resolution details and avg time-to-resolution (last 7 days)
-
-**17 Template Resources** (9 base templates + 8 dynamic `{repo}` variants):
-
-- `memory://projects/{number}/timeline` - Project activity timeline
-- `memory://issues/{issue_number}/entries` - Entries linked to issue
-- `memory://prs/{pr_number}/entries` - Entries linked to PR
-- `memory://prs/{pr_number}/timeline` - Combined PR + journal timeline
-- `memory://kanban/{project_number}` - GitHub Project Kanban board
-- `memory://kanban/{project_number}/diagram` - Kanban Mermaid visualization
-- `memory://milestones/{number}` - Milestone detail with completion progress
-- `memory://help/{group}` - Per-group tool reference with parameters and annotations
-- `memory://briefing/{repo}` - Context targeted to a specific repository
-
-_Note: The `memory://github/status`, `memory://github/insights`, `memory://github/milestones`, and `memory://milestones/{number}` resources also accept an optional `/{repo}` path suffix for cross-repo targeting._
+### 🎯 **Workflow Prompts**
+
+Specialized workflow prompts cover session briefing, standup & retro prep, goal tracking, PR & issue command, session summaries, and journal optimization. Additional prompts support CMS REM supervision, adversarial plan reviews, code & security audits, secure commit workflows, and anti-hallucination healing. **[Complete prompts guide →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Prompts)**
+
+### 📡 **Resources**
+See the **[Complete resources guide →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Resources)** for the full list of dynamic context resources, including `memory://briefing`, `memory://instructions`, GitHub integration endpoints, telemetry metrics, and templated views.
+
+- **Dynamic Resource Templates**: Resources `memory://briefing/{+repo}`, `memory://agent-context/{+repo}`, `memory://agent-id/{+repo}`, `memory://actions/recent/{+repo}`, `memory://github/status/{+repo}`, `memory://github/milestones/{+repo}`, `memory://milestones/{+repo}/{number}`, and `memory://kanban/{+repo}/{project_number}` accept an RFC 6570 `{+repo}` path parameter for targeted project context.
 
 ---
 
 ## ⚡ Code Mode: Maximum Efficiency (90% Token Savings)
 
-Code Mode (`mj_execute_code`) is a revolutionary approach that **dramatically reduces token usage by up to 90%** and is included by default in all presets. Instead of spending thousands of tokens on sequential tool calls, AI agents use a single sandboxed execution to reason faster.
+Code Mode (`mj_execute_code`) **reduces token usage by up to 90%** and is included by default in all presets. Instead of spending thousands of tokens on sequential tool calls, AI agents use a single sandboxed execution to reason faster.
 
-Code executes in a **worker_threads sandbox** designed as a secure multi-tenant process isolation environment. All `mj.*` API calls execute against the journal within the sandbox, providing:
+Code executes in a **pre-warmed `worker_threads` V8 isolate pool + secondary `vm.createContext` boundary** designed as a secure multi-tenant process isolation environment. All `mj.*` API calls execute against the journal within the sandbox, providing:
 
 - **V8 code generation restrictions** — `eval()` and `Function()` construction from strings disabled at the V8 engine level via `codeGeneration: { strings: false, wasm: false }`
-- **Frozen prototypes** — all built-in prototypes (Object, Function, Array, Error, etc.) frozen inside the vm context to prevent dynamic constructor chain escapes
-- **Static code validation** — 18 regex rules blocking `require()`, `process`, `eval()`, `Reflect.*`, `Symbol.*`, `new Proxy()`, and filesystem/network access
+- **Frozen prototypes & cross-realm constructor lockdown** — all built-in prototypes (`Object`, `Function`, `Array`, `Error`, etc.) and `mj.*` API bindings are frozen, and `.constructor` is neutered across `Object`, `Function`, `AsyncFunction`, `GeneratorFunction`, and `AsyncGeneratorFunction` prototypes in both the inner `vm` realm and outer worker realm to prevent dynamic constructor chain escapes
+- **Single-pass lexical validation** — pre-validation rate-limiting and 50KB byte caps run before any code normalization, followed by a single-pass lexical comment/string scanner (preserving `${...}` template expressions) and static rules blocking `require()`, `import()`, `process`, `eval()`, `Reflect.*`, `Symbol.*`, `Object.getPrototypeOf`/`setPrototypeOf`/`defineProperty`, `new Proxy()`, and filesystem/network access
 - **Proxy constructor nullified** — `Proxy: undefined` in the sandbox prevents meta-object protocol abuse
-- **RPC allowlist** — host-side validation prevents workers from invoking unauthorized API methods
+- **Prototype-safe RPC allowlist** — host-side `Object.hasOwn()` validation, recursion-bounded argument normalization, and `--tool-filter` enforcement prevent workers from invoking unauthorized or filtered API methods
 - **Rate limiting** — 60 executions per minute per client
-- **Hard timeouts** — configurable execution limit (default 30s)
-- **Egress boundary enforcement** — result serialization capped to prevent OOM via oversized payloads
-- **Full API access** — all 10 tool groups are available via `mj.*` (e.g., `mj.core.createEntry()`, `mj.search.searchEntries()`, `mj.github.getGithubIssues()`, `mj.team.passTeamFlag()`)
+- **Hard timeouts** — configurable execution limit (default 30s) with bounded async timer tracking (`setTimeout`/`sleep` capped and cleared on completion)
+- **Egress boundary enforcement** — result serialization capped (default 100KB via `CODE_MODE_MAX_RESULT_SIZE`) with automatic payload compaction to prevent OOM via oversized payloads
+- **Full API access** — all tool groups are available via `mj.*` (e.g., `mj.core.createEntry()`, `mj.search.searchEntries()`, `mj.github.getGithubIssues()`)
 - **Strict Readonly Contract** — Calling any mutation method under `--tool-filter readonly` safely halts the sandbox to prevent execution, returning a structured `{ success: false, error: "..." }` response to the agent instead of a raw MCP protocol exception.
 
-### ⚡ Code Mode Only (Maximum Token Savings)
+### ⚡ Code Mode Minimal Surface (Maximum Token Savings)
 
-Run with **only Code Mode enabled** — a single tool that provides access to all 69 tools' worth of capability through the `mj.*` API:
+Run with the `codemode` filter and `--codemode-internal-full-access` to expose only the escape-hatch tools (`mj_execute_code` and `update_configuration`) on the MCP tool list while retaining full internal access to the `mj.*` API inside the sandbox:
 
 ```json
 {
   "mcpServers": {
     "memory-journal-mcp": {
       "command": "memory-journal-mcp",
-      "args": ["--tool-filter", "codemode"]
+      "args": ["--tool-filter", "codemode", "--codemode-internal-full-access"]
     }
   }
 }
 ```
 
-This exposes just `mj_execute_code`. The agent writes JavaScript against the typed `mj.*` SDK — composing operations across all 10 tool groups and returning exactly the data it needs — in one execution. This mirrors the [Code Mode pattern](https://blog.cloudflare.com/code-mode-mcp/) pioneered by Cloudflare for their entire API: fixed token cost regardless of how many capabilities exist.
-
-#### Disabling Code Mode
-
-If you prefer individual tool calls, exclude codemode:
-
-```json
-{
-  "args": ["--tool-filter", "starter,-codemode"]
-}
-```
+This exposes only `mj_execute_code` and `update_configuration` to the client's `tools/list`, reducing tool schema overhead to the minimum while preserving full programmatic capability via `mj.*`. The agent writes JavaScript against the typed `mj.*` SDK — composing operations across all tool groups and returning exactly the data it needs — in one execution. This mirrors the [Code Mode pattern](https://blog.cloudflare.com/code-mode-mcp/) pioneered by Cloudflare for their entire API: fixed token cost regardless of how many capabilities exist. Without `--codemode-internal-full-access` (or `CODEMODE_INTERNAL_FULL_ACCESS=true`), internal `mj.*` methods are scoped to the active `--tool-filter`.
 
 ---
 
-## 🤫 Hush Protocol: Asynchronous Team Collaboration
+## 🚀 Quick Start & Deployment
 
-The **Hush Protocol** reimagines team collaboration for AI-augmented workflows by replacing noisy Slack/Teams messages with structured, machine-actionable flags.
+_Note: Configuration is resolved using strict precedence: `CLI flags > Environment Variables > Config File > Defaults`._
 
-When you encounter a blocker, need a review, or want to broadcast a milestone, your AI agent can raise a flag in the shared Team Database:
+> 🛠️ **Debugging Configuration:** Run `memory-journal-mcp --dump-config` (or pass `--dump-config` as an arg) to print the fully resolved configuration payload with automatically redacted secrets. This is the primary method for diagnosing overriding issues.
 
-- **Actionable Visibility**: Active flags automatically surface at the very top of the `memory://briefing` payload for all team members. When another developer's agent starts a session, it immediately sees your blockers and can help resolve them autonomously.
-- **Structured Types**: Raise specific flag types (`blocker`, `needs_review`, `help_requested`, `fyi`). You can customize your team's vocabulary via the `--flag-vocabulary` configuration.
-- **Searchable History**: Unlike chat messages that disappear into the void, Hush flags are permanent, query-able AI journal entries. Your agents can search past `needs_review` flags to understand how architectural blockers were conquered.
-- **Integrated Standup & Retro Signals**: Active flags automatically appear as contextual signals in the `prepare-standup` and `prepare-retro` prompts, so your daily standups and sprint retrospectives always surface outstanding blockers.
-- **Full Lifecycle Management**: List and filter flags by status, type, or assignee via `team_list_flags`. Update metadata (escalate severity, reassign, add links) or reopen resolved flags via `team_update_flag`. Track resolution velocity, per-user workload, and trends with `team_get_flag_analytics`.
+### Configure Basics Quickly
 
-**Dashboard & Operations**: Read `memory://flags` for an active dashboard, `memory://flags/history` for recently resolved flags, use the `/flag-dashboard` prompt for guided triage with severity grouping and staleness detection, and use `mj.team.passTeamFlag()` / `mj.team.resolveTeamFlag()` / `mj.team.teamListFlags()` / `mj.team.teamUpdateFlag()` / `mj.team.teamGetFlagAnalytics()` to manage flags programmatically in Code Mode.
-
-**[Complete Hush Protocol guide and Mermaid sequence diagrams →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Hush-Protocol)**
-
----
-
-## 🚀 Quick Start
-
-### Option 1: npm (Recommended)
-
-```bash
-npm install -g memory-journal-mcp
-```
-
-### Option 2: From Source
-
-```bash
-git clone https://github.com/neverinfamous/memory-journal-mcp.git
-cd memory-journal-mcp
-npm install
-npm run build
-```
-
-### Add to MCP Config
-
-Add this to your `~/.cursor/mcp.json`, Claude Desktop config, or equivalent:
-
-### Basic Configuration
+> 💡 **Tip:** Don't want to manually escape JSON strings for `PROJECT_REGISTRY`? Run `npx memory-journal-mcp project create <name> --path <repo-path> [--number <project-number>]` in your terminal to automatically bootstrap and update your MCP configuration!
 
 ```json
 {
@@ -361,10 +265,12 @@ Add this to your `~/.cursor/mcp.json`, Claude Desktop config, or equivalent:
 }
 ```
 
-### Advanced Configuration (Recommended)
+### Power Up with Advanced Configuration
 
 Showcasing the full power of the server, including Multi-Project Routing, Team Collaboration, Copilot awareness, and Context Injections.
 
+> 💡 **Tip:** Use `npx memory-journal-mcp project create <name> --path <repo-path> [--number <project-number>]` to easily configure multiple repositories into your `PROJECT_REGISTRY` without manual JSON escaping!
+
 ```json
 {
   "mcpServers": {
@@ -407,19 +313,19 @@ The `memory://briefing` resource is **dynamically assembled** at each session st
 
 - **System State:** Server version, capability statuses, resource/tool counts, test health, and `memory://metrics/summary` breadcrumbs.
 - **Repository Context:** Git working tree status, unreleased changes, exact code-map paths, and prioritized gatekeeper CI workflows.
-- **Ambient Context:** Active workspace paths, local time, analytics, and active Hush Protocol flags.
+- **Ambient Context:** Active workspace paths, local time, analytics.
 
 You control exactly what additional content your agent sees across three dimensions:
 
 | Dimension             | Variables                                                                                                                                                                        | What It Controls                                                                    |
 | --------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- |
-| **Depth**             | `INSTRUCTION_LEVEL`                                                                                                                                                              | Behavioral guidance verbosity: `essential`, `standard` (default), `full`            |
-| **Journal Content**   | `BRIEFING_ENTRY_COUNT`, `BRIEFING_SUMMARY_COUNT`, `BRIEFING_INCLUDE_TEAM`                                                                                                        | How many recent entries, session summaries, and whether team entries appear         |
+| **Focus**             | `MEMORY_JOURNAL_MCP_TOOL_FILTER` (CLI: `--tool-filter`, config: `"toolFilter"`)                                                                                                  | Control tool exposure: `full` (default), `starter`, `essential`, `readonly`, `codemode` |
+| **Journal Content**   | `BRIEFING_ENTRY_COUNT`, `BRIEFING_SUMMARY_COUNT`, `BRIEFING_COMMIT_COUNT`, `BRIEFING_IMPORTANCE_THRESHOLD`, `BRIEFING_INCLUDE_TEAM`                                              | How many recent entries, session summaries, commits, and whether team entries appear |
 | **GitHub Enrichment** | `BRIEFING_ISSUE_COUNT`, `BRIEFING_PR_COUNT`, `BRIEFING_PR_STATUS`, `BRIEFING_MILESTONE_COUNT`, `BRIEFING_WORKFLOW_COUNT`, `BRIEFING_WORKFLOW_STATUS`, `BRIEFING_COPILOT_REVIEWS` | Issues, PRs, milestones, CI runs, and Copilot review state surfaced in the briefing |
 
 **Context Injections:** Set `RULES_FILE_PATH` and `SKILLS_DIR_PATH` to surface user rules and agent skills as companion resources (`memory://rules`, `memory://skills`) alongside the briefing.
 
-**Repo Targeting:** In multi-repo setups, agents read `memory://briefing/{repo}` to get a briefing scoped to a specific repository registered in `PROJECT_REGISTRY`.
+**Repo Targeting:** In multi-repo setups, agents read `memory://briefing/{+repo}` to get a briefing scoped to a specific repository registered in `PROJECT_REGISTRY`.
 
 <details>
 <summary><strong>Briefing Presets (click to expand)</strong></summary>
@@ -429,7 +335,7 @@ You control exactly what additional content your agent sees across three dimensi
 ```json
 "BRIEFING_ENTRY_COUNT": "1",
 "BRIEFING_SUMMARY_COUNT": "0",
-"INSTRUCTION_LEVEL": "essential"
+"MEMORY_JOURNAL_MCP_TOOL_FILTER": "essential"
 ```
 
 **Full Context (onboarding agents)** — Maximize context for agents unfamiliar with the project:
@@ -442,7 +348,7 @@ You control exactly what additional content your agent sees across three dimensi
 "BRIEFING_PR_COUNT": "3",
 "BRIEFING_PR_STATUS": "true",
 "BRIEFING_COPILOT_REVIEWS": "true",
-"INSTRUCTION_LEVEL": "full"
+"MEMORY_JOURNAL_MCP_TOOL_FILTER": "full"
 ```
 
 **DevOps-Heavy** — Emphasize CI/CD and GitHub state for infrastructure workflows:
@@ -467,50 +373,57 @@ You control exactly what additional content your agent sees across three dimensi
 | **Minimal (no GitHub)** | Remove the `env` block entirely                                                                                              |
 | **npx (no install)**    | Replace `"command"` with `"npx"` and add `"args": ["-y", "memory-journal-mcp"]`                                              |
 | **From source**         | Replace `"command"` with `"node"` and add `"args": ["dist/cli.js"]`                                                          |
-| **Code Mode only**      | Add `"args": ["--tool-filter", "codemode"]` (single tool, all capabilities)                                                  |
-| **Docker**              | Replace `"command"` with `"docker"` and use `run -i --rm -v ./data:/app/data writenotenow/memory-journal-mcp:latest` as args |
+| **Code Mode minimal**   | Add `"args": ["--tool-filter", "codemode", "--codemode-internal-full-access"]` (`mj_execute_code` + `update_configuration`, all `mj.*` capabilities) |
+| **Docker**              | Replace `"command"` with `"docker"` and add `"args": ["run", "-i", "--rm", "-v", "./data:/app/data", "-e", "GITHUB_TOKEN", "-e", "PROJECT_REGISTRY", "-e", "ALLOWED_IO_ROOTS", "writenotenow/memory-journal-mcp:latest"]` (forward any `"env"` keys via `-e <VAR>`) |
 | **Team collaboration**  | Add `"TEAM_DB_PATH": "./team.db"` to `env`                                                                                   |
 
 Restart your MCP client and start journaling!
 
-### Option 3: HTTP/SSE Transport (Remote Access)
+### Connect Remotely with HTTP/SSE Transport
 
-> 🔒 **Security Posture: Stdio vs HTTP**
+> [!IMPORTANT]
+> **Security Posture: Stdio vs HTTP (Fail-Closed Startup Guards)**
 >
-> - **Stdio (Default):** Runs implicitly within the secure boundaries of your local IDE or command-line environment. No explicit authentication is required because the execution context is already trusted.
-> - **HTTP/SSE:** Exposes the server over a network socket. By default, HTTP binds ONLY to `localhost` and blocks wildcard CORS to prevent unauthorized access and CSRF attacks. **Public network binding (`--server-host 0.0.0.0`) requires explicit authentication** (`--auth-token` or `--oauth-enabled`). The server will throw a fatal error if you attempt to expose it publicly without securing it.
+> - **Stdio (Default):** Runs implicitly within the secure boundaries of your local IDE or command-line environment. No explicit authentication is required because the execution context is already trusted (`ALLOWED_IO_ROOTS` defaults to fail-closed `[]` unless configured).
+> - **HTTP/SSE (`--transport http`):** Exposes the server over a network socket and enforces **three fail-closed startup guards**:
+>   1. **Mandatory Filesystem Boundary (`ALLOWED_IO_ROOTS` / `--allowed-io-roots`):** Always required in HTTP mode so filesystem boundaries are explicitly declared.
+>   2. **Mandatory Public Authentication:** By default, HTTP binds ONLY to `localhost` and blocks wildcard CORS to prevent unauthorized access and CSRF attacks. Binding to a non-loopback address (`--server-host 0.0.0.0`) requires explicit authentication (`MCP_AUTH_TOKEN` / `--auth-token` or `--oauth-enabled`).
+>   3. **Mandatory Public Origin for Non-Loopback OAuth (`PUBLIC_ORIGIN` / `--public-origin`):** When `--oauth-enabled` is bound to a non-loopback address, `--public-origin` (`PUBLIC_ORIGIN`) is strictly required so RFC 9728 Protected Resource Metadata cannot be spoofed via `Host` headers.
 
 For remote access or web-based clients, run the server in HTTP mode:
 
 ```bash
-memory-journal-mcp --transport http --port 3000
+memory-journal-mcp --transport http --port 3000 --allowed-io-roots /path/to/allowed/dir
 ```
 
-To bind to all interfaces (required for containers) and enable the automated proactive analytics scheduler (e.g. daily digest), you MUST provide an authentication token:
+To bind to all interfaces (required for containers) and enable the automated proactive analytics scheduler (e.g. daily digest), you MUST provide both `ALLOWED_IO_ROOTS` and an authentication token:
 
 ```bash
 export MCP_AUTH_TOKEN="your_secure_random_token"
+export MCP_AUTH_SCOPES="full" # Defaults to "read" if omitted
+export ALLOWED_IO_ROOTS="/path/to/allowed/dir"
 memory-journal-mcp --transport http --port 3000 --server-host 0.0.0.0 --digest-interval 1440
 ```
 
 **Endpoints:**
 
-| Endpoint                                    | Description                                      | Mode     |
-| ------------------------------------------- | ------------------------------------------------ | -------- |
-| `GET /`                                     | Server info and available endpoints              | Both     |
-| `POST /mcp`                                 | JSON-RPC requests (initialize, tools/call, etc.) | Both     |
-| `GET /mcp`                                  | SSE stream for server-to-client notifications    | Stateful |
-| `DELETE /mcp`                               | Session termination                              | Stateful |
-| `GET /sse`                                  | Legacy SSE connection (MCP 2024-11-05)           | Stateful |
-| `POST /messages`                            | Legacy SSE message endpoint                      | Stateful |
-| `GET /health`                               | Health check (`{ status, timestamp }`)           | Both     |
-| `GET /.well-known/oauth-protected-resource` | RFC 9728 Protected Resource Metadata             | Both     |
+| Endpoint                                    | Description                                                        | Mode     |
+| ------------------------------------------- | ------------------------------------------------------------------ | -------- |
+| `GET /`                                     | Server info and available endpoints                                | Both     |
+| `POST /mcp`                                 | JSON-RPC requests (initialize, tools/call, etc.)                   | Both     |
+| `GET /mcp`                                  | SSE stream for server-to-client notifications                      | Stateful |
+| `DELETE /mcp`                               | Session termination (`204 No Content`)                             | Both     |
+| `GET / POST /sse`                           | Legacy SSE connection & stateless/stateful POST (MCP 2024-11-05)   | GET: Stateful / POST: Both |
+| `POST /messages`                            | Legacy SSE message endpoint                                        | Stateful |
+| `GET /health`                               | Health check (`{ status, timestamp }`)                             | Both     |
+| `GET /metrics`                              | Prometheus metrics export (requires flag)                          | Both     |
+| `GET /.well-known/oauth-protected-resource` | RFC 9728 Protected Resource Metadata (requires `--oauth-enabled`)  | Both     |
 
 **Session Management:** The server uses stateful sessions by default. Include the `mcp-session-id` header (returned from initialization) in subsequent requests.
 
 - **OAuth 2.1** — RFC 9728/8414, JWT/JWKS, granular scopes (opt-in via `--oauth-enabled`)
-- **7 Security Headers** — CSP, HSTS (opt-in), X-Frame-Options, and more
-- **Rate Limiting** — 100 req/min per IP · **CORS** — configurable multi-origin (exact-match) · **1MB body limit**
+- **Comprehensive Security Headers** — CSP, HSTS (opt-in), X-Frame-Options, and more
+- **Rate Limiting** — 100 req/min per subject/IP · **CORS** — configurable multi-origin (exact-match) · **1MB body limit**
 - **Server Timeouts** — Request (120s), keep-alive (65s), headers (66s) · **404 handler** · **Cross-protocol guard**
 - **Build Provenance** · **SBOM** · **Supply Chain Attestations** · **Non-root execution**
 
@@ -540,7 +453,7 @@ curl -X POST http://localhost:3000/mcp \
 For serverless deployments (Lambda, Workers, Vercel), use stateless mode:
 
 ```bash
-memory-journal-mcp --transport http --port 3000 --stateless
+memory-journal-mcp --transport http --port 3000 --stateless --allowed-io-roots /path/to/projects
 ```
 
 | Mode                      | Progress Notifications | Legacy SSE | Serverless |
@@ -556,84 +469,39 @@ When running in HTTP/SSE mode, enable periodic maintenance jobs with CLI flags.
 
 ```bash
 memory-journal-mcp --transport http --port 3000 \
+  --allowed-io-roots /path/to/projects \
   --backup-interval 60 --keep-backups 10 \
   --vacuum-interval 1440 \
   --rebuild-index-interval 720
 ```
 
-| Flag                             | Default | Description                                                          |
-| -------------------------------- | ------- | -------------------------------------------------------------------- |
-| `--backup-interval <min>`        | 0 (off) | Create timestamped database backups and prune old ones automatically |
-| `--keep-backups <count>`         | 5       | Max backups retained during automated cleanup                        |
-| `--vacuum-interval <min>`        | 0 (off) | Run `PRAGMA optimize` and flush database to disk                     |
-| `--rebuild-index-interval <min>` | 0 (off) | Full vector index rebuild to maintain semantic search quality        |
+| Flag                                    | Default                  | Description                                                           |
+| --------------------------------------- | ------------------------ | --------------------------------------------------------------------- |
+| `--backup-interval <min>`               | 0 (off)                  | Create timestamped database backups and prune old ones automatically  |
+| `--keep-backups <count>`                | 5                        | Max backups retained during automated cleanup                         |
+| `--vacuum-interval <min>`               | 0 (off)                  | Run `PRAGMA optimize` and flush database to disk                      |
+| `--rebuild-index-interval <min>`        | 0 (off)                  | Full vector index rebuild to maintain semantic search quality         |
+| `--report-interval <min>`               | 0 (off)                  | Scheduled report generation interval in minutes                       |
+| `--report-webhook-url <url>`            | —                        | HTTPS webhook URL for scheduled report delivery                       |
+| `--report-webhook-auth <header>`        | —                        | Custom `Authorization` header for webhook requests                    |
+| `--report-content-type <type>`          | `slack`                  | Webhook payload format: `slack`, `discord`, or `json` (env: `REPORT_CONTENT_TYPE`) |
+| `--digest-interval <min>`               | 0 (off)                  | Scheduled periodic digest analysis report                             |
+| `--auto-prune-interval <min>`           | 0 (off)                  | Run autonomous garbage collection (archive, soft-delete, hard-delete) |
+| `--archive-older-than-days <days>`      | 0 (off)                  | Auto-archive low-importance entries older than N days                 |
+| `--prune-older-than-days <days>`        | 0 (off)                  | Auto soft-delete entries older than N days                            |
+| `--hard-delete-older-than-days <days>`  | 0 (off)                  | Permanently purge soft-deleted entries older than N days              |
+| `--prune-importance-threshold <score>`  | 0.15                     | Max importance score (`0.0`–`1.0`) eligible for archiving/pruning     |
+| `--prune-dry-run`                       | false                    | Log auto-prune candidates without mutating entries                    |
+| `--prune-exclude-tags <tags>`           | —                        | Comma-separated tags exempt from auto-prune (`archived` always kept)  |
 
 Each job is error-isolated — a failure in one job won't affect the others. Scheduler status (last run, result, next run) is visible via `memory://health`.
 
-### GitHub Integration Configuration
+### Integrate Seamlessly with GitHub
 
 The GitHub tools (`get_github_issues`, `get_github_prs`, etc.) auto-detect the repository from your git context when `PROJECT_REGISTRY` is configured or the MCP server is run inside a git repository.
 
-| Environment Variable              | Description                                                                                                                                           |
-| --------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `DB_PATH`                         | Database file location (CLI: `--db`; default: `./memory_journal.db`)                                                                                  |
-| `TEAM_DB_PATH`                    | Team database file location (CLI: `--team-db`)                                                                                                        |
-| `TEAM_AUTHOR`                     | Override author name for team entries (default: `git config user.name`)                                                                               |
-| `GITHUB_TOKEN`                    | GitHub personal access token for API access                                                                                                           |
-| `DEFAULT_PROJECT_NUMBER`          | Default GitHub Project number for auto-assignment when creating issues                                                                                |
-| `PROJECT_REGISTRY`                | JSON map of repos to `{ path, project_number }` for multi-project auto-detection and routing                                                          |
-| `AUTO_REBUILD_INDEX`              | Set to `true` to rebuild vector index on server startup                                                                                               |
-| `MCP_HOST`                        | Server bind host (`0.0.0.0` for containers, default: `localhost`)                                                                                     |
-| `MCP_AUTH_TOKEN`                  | Bearer token for HTTP transport authentication (CLI: `--auth-token`). Must NOT be the default placeholder token.                                      |
-| `ALLOWED_IO_ROOTS`                | **Critical Security Boundary**: Comma-separated absolute paths granting filesystem access to Code Mode and export tools (default: none / fail-closed) |
-| `MCP_CORS_ORIGIN`                 | Allowed CORS origins for HTTP transport, comma-separated (default: blank, strict opt-in)                                                              |
-| `TRUST_PROXY`                     | Trust proxy headers for rate limiting and origin checks (CLI: `--trust-proxy`; default: `false`)                                                      |
-| `PUBLIC_ORIGIN`                   | Public origin URL for OAuth redirect URIs (CLI: `--public-origin`)                                                                                    |
-| `MCP_RATE_LIMIT_MAX`              | Max requests per minute per client IP, HTTP only (default: `100`)                                                                                     |
-| `LOG_LEVEL`                       | Log verbosity: `error`, `warn`, `info`, `debug` (default: `info`; CLI: `--log-level`)                                                                 |
-| `MCP_ENABLE_HSTS`                 | Enable HSTS security header on HTTP responses (CLI: `--enable-hsts`; default: `false`)                                                                |
-| `OAUTH_ENABLED`                   | Set to `true` to enable OAuth 2.1 authentication (HTTP only)                                                                                          |
-| `OAUTH_ISSUER`                    | OAuth issuer URL (e.g., `https://auth.example.com/realms/mcp`)                                                                                        |
-| `OAUTH_AUDIENCE`                  | Expected JWT audience claim                                                                                                                           |
-| `OAUTH_JWKS_URI`                  | JWKS endpoint for token signature verification                                                                                                        |
-| `OAUTH_ALLOW_PLAINTEXT_LOOPBACK`  | Allow plaintext HTTP loopback redirect URIs for local OAuth clients (CLI: `--oauth-allow-plaintext-loopback`; default: `false`)                       |
-| `OAUTH_CLOCK_TOLERANCE`           | Allowed clock skew tolerance in seconds for JWT verification (default: `5`)                                                                           |
-| `CODE_MODE_MAX_RESULT_SIZE`       | Maximum size in bytes for mj_execute_code result payload (CLI: `--codemode-max-result-size`; default: `102400`)                                       |
-| `CODEMODE_INTERNAL_FULL_ACCESS`   | Bypass tool filter constraints within the Code Mode sandbox (CLI: `--codemode-internal-full-access`; default: `false`)                                |
-| `BRIEFING_ENTRY_COUNT`            | Journal entries in briefing (CLI: `--briefing-entries`; default: `3`)                                                                                 |
-| `BRIEFING_SUMMARY_COUNT`          | Session summaries to list in briefing (CLI: `--briefing-summaries`; default: `1`)                                                                     |
-| `BRIEFING_INCLUDE_TEAM`           | Include team DB entries in briefing (`true`/`false`; default: `false`)                                                                                |
-| `BRIEFING_ISSUE_COUNT`            | Issues to list in briefing; `0` = count only (default: `0`)                                                                                           |
-| `BRIEFING_PR_COUNT`               | PRs to list in briefing; `0` = count only (default: `0`)                                                                                              |
-| `BRIEFING_PR_STATUS`              | Show PR status breakdown (open/merged/closed; default: `false`)                                                                                       |
-| `BRIEFING_MILESTONE_COUNT`        | Milestones to list in briefing; `0` = hide entirely (CLI: `--briefing-milestones`; default: `3`)                                                      |
-| `BRIEFING_WORKFLOW_COUNT`         | Workflow runs to list in briefing; `0` = status only (default: `0`)                                                                                   |
-| `BRIEFING_WORKFLOW_STATUS`        | Show workflow status breakdown in briefing (default: `false`)                                                                                         |
-| `BRIEFING_COPILOT_REVIEWS`        | Aggregate Copilot review state in briefing (default: `false`)                                                                                         |
-| `RULES_FILE_PATH`                 | Path to user rules file for agent awareness (CLI: `--rules-file`)                                                                                     |
-| `SKILLS_DIR_PATH`                 | Path to skills directory for agent awareness (CLI: `--skills-dir`)                                                                                    |
-| `MEMORY_JOURNAL_WORKFLOW_SUMMARY` | Free-text workflow summary for `memory://workflows` (CLI: `--workflow-summary`)                                                                       |
-| `INSTRUCTION_LEVEL`               | Briefing depth: `essential`, `standard`, `full` (CLI: `--instruction-level`; default: `standard`)                                                     |
-| `PROJECT_LINT_CMD`                | Project lint command for GitHub Commander validation gates (default: `npm run lint`)                                                                  |
-| `PROJECT_TYPECHECK_CMD`           | Project typecheck command (default: `npm run typecheck`; empty = skip)                                                                                |
-| `PROJECT_BUILD_CMD`               | Project build command (default: `npm run build`; empty = skip)                                                                                        |
-| `PROJECT_TEST_CMD`                | Project test command (default: `npm run test`)                                                                                                        |
-| `PROJECT_E2E_CMD`                 | Project E2E test command (default: empty = skip)                                                                                                      |
-| `PROJECT_PACKAGE_MANAGER`         | Package manager override: `npm`, `yarn`, `pnpm`, `bun` (default: auto-detect from lockfile)                                                           |
-| `PROJECT_HAS_DOCKERFILE`          | Enable Docker audit steps (default: auto-detect)                                                                                                      |
-| `COMMANDER_HITL_FILE_THRESHOLD`   | Human-in-the-loop checkpoint if changes touch > N files (default: `10`)                                                                               |
-| `COMMANDER_SECURITY_TOOLS`        | Override security tool auto-detection (comma-separated; default: auto-detect)                                                                         |
-| `COMMANDER_BRANCH_PREFIX`         | Branch naming prefix for PRs (default: `fix`)                                                                                                         |
-| `AUDIT_LOG_PATH`                  | Path for the JSONL operational telemetry log of write/admin tool calls. Rotates at 10 MB (keeps 5 archives). Omit to disable telemetry logging.       |
-| `AUDIT_REDACT`                    | Set to `false` to include tool arguments in telemetry log entries (default: `true`)                                                                   |
-| `AUDIT_READS`                     | Log read-scoped tool calls in addition to write/admin (CLI: `--audit-reads`; default: `false`)                                                        |
-| `AUDIT_LOG_MAX_SIZE`              | Maximum operational telemetry file size in bytes before rotation (CLI: `--audit-log-max-size`; default: `10485760`)                                   |
-| `MCP_METRICS_ENABLED`             | Set to `false` to disable in-memory tool call metrics accumulation (default: `true`)                                                                  |
-| `FLAG_VOCABULARY`                 | Comma-separated flag types for Hush Protocol (CLI: `--flag-vocabulary`; default: `blocker,needs_review,help_requested,fyi`)                           |
-| `PRUNE_OLDER_THAN_DAYS`           | Soft-delete entries older than N days with importance below threshold on startup; `0` = disabled (CLI: `--prune-older-than-days`; default: `0`)       |
-| `PRUNE_IMPORTANCE_THRESHOLD`      | Importance score threshold (0.0–1.0) — entries scoring below this are pruned (CLI: `--prune-importance-threshold`; default: `0.15`)                   |
-
-**Multi-Project Workflows**: For agents to seamlessly support multiple projects, provide **`PROJECT_REGISTRY`**.
+
+**Multi-Project Workflows**: For agents to seamlessly support multiple projects, configure your **`PROJECT_REGISTRY`** (tip: use `npx memory-journal-mcp project create <name> --path <repo-path> [--number <project-number>]`).
 
 #### Dynamic Context Resolution & Auto-Detection
 
@@ -641,7 +509,7 @@ When executing GitHub tools (issues, PRs, context, etc.), the server resolves re
 
 1. **Dynamic Project Routing**: If the agent passes a `repo` string that matches a key in your `PROJECT_REGISTRY`, the server dynamically mounts the physical directory mapped to that project. It executes git commands locally and automatically infers the `owner`.
 2. **Explicit Override**: If the agent provides both `owner` and `repo` explicitly, those values override auto-detection for API calls.
-3. **Missing Context**: Without `PROJECT_REGISTRY` or explicit parameters, the server blocks execution and returns `{requiresUserInput: true}` to prompt the agent.
+3. **Missing Context**: Without `PROJECT_REGISTRY` or explicit parameters, the server blocks execution and returns `{requiresUserInput: true}` to prompt the agent. If an agent encounters this blocked state, it can seamlessly recover by invoking the `mj.admin.registerProject()` method via Code Mode to auto-configure the project registry on the fly.
 
 #### Automatic Project Routing (Kanban / Issues)
 
@@ -660,21 +528,25 @@ For production deployments, enable OAuth 2.1 authentication on the HTTP transpor
 | Protected Resource Metadata | ✅     | RFC 9728 `/.well-known/oauth-protected-resource` |
 | Auth Server Discovery       | ✅     | RFC 8414 metadata discovery with caching         |
 | Token Validation            | ✅     | JWT validation with JWKS support                 |
-| Scope Enforcement           | ✅     | Granular `read`, `write`, `admin` scopes         |
+| Scope Enforcement           | ✅     | Granular `read`, `write`, `team`, `audit`, `admin`, `full` scopes |
 | HTTP Transport              | ✅     | Streamable HTTP with OAuth middleware            |
 
 **Supported Scopes:**
 
-| Scope   | Tool Groups                                       |
-| ------- | ------------------------------------------------- |
-| `read`  | core, search, analytics, relationships, io        |
-| `write` | github, team (+ all read groups)                  |
-| `admin` | admin, backup, codemode (+ all write/read groups) |
+| Scope   | Tool Groups                                                        |
+| ------- | ------------------------------------------------------------------ |
+| `read`  | `core (read-only), search, analytics, relationships (visualize_relationships), io (export_entries), git` |
+| `write` | `github (+ all read groups and create_entry / create_entry_minimal / link_entries / mark_anchors_stale / import_external / import_markdown / export_markdown)` |
+| `team`  | `team (dedicated team collaboration scope; combine with read/write for personal journal access)` |
+| `audit` | `memory://audit resource access (included in admin/full; search_audit_log requires admin or full)` |
+| `admin` | `admin, backup, codemode (+ all read/write/team/audit groups)`     |
+| `full`  | `Unrestricted access to all operations`                            |
 
 **Quick Start:**
 
 ```bash
 memory-journal-mcp --transport http --port 3000 \
+  --allowed-io-roots /path/to/projects \
   --oauth-enabled \
   --oauth-issuer https://auth.example.com/realms/mcp \
   --oauth-audience memory-journal-mcp \
@@ -684,10 +556,12 @@ memory-journal-mcp --transport http --port 3000 \
 Or via environment variables:
 
 ```bash
+export ALLOWED_IO_ROOTS="/path/to/projects"
 export OAUTH_ENABLED=true
 export OAUTH_ISSUER=https://auth.example.com/realms/mcp
 export OAUTH_AUDIENCE=memory-journal-mcp
-export OAUTH_CLOCK_TOLERANCE=5
+export OAUTH_JWKS_URI=https://auth.example.com/realms/mcp/protocol/openid-connect/certs
+export OAUTH_CLOCK_TOLERANCE=60
 memory-journal-mcp --transport http --port 3000
 ```
 
@@ -701,6 +575,59 @@ memory-journal-mcp --transport http --port 3000
 
 ## 🔧 Configuration
 
+### Environment Variables
+
+| Variable                                       | Description                                                |
+| ---------------------------------------------- | ---------------------------------------------------------- |
+| **Core Database & Server** | |
+| `DB_PATH`                                      | Path to the personal journal SQLite database (CLI: `--db`, `--database`, default: `./memory_journal.db`) |
+| `DB_ENCRYPTION_KEY`                            | SQLCipher at-rest database encryption key (alias: `MJ_DB_ENCRYPTION_KEY`) |
+| `TEAM_DB_PATH`                                 | Path to the shared team SQLite database (CLI: `--team-db`, `--team-database`) |
+| `TEAM_AUTHOR`                                  | Display name attached to team entries (used for local author identity; OAuth identity claims take precedence when creating team entries and RBAC ownership under active OAuth) |
+| `TEAM_DEFAULT_ROLE`                            | Default RBAC role for unlisted team authors: `admin`, `member`, `viewer`, `denied` (CLI: `--team-default-role`, default: `denied`) |
+| `TEAM_ADMIN`                                   | Bootstrap admin author name when the `team_members` table is empty (CLI: `--team-admin`) |
+| `ADDITIONAL_TEAM_DBS`                          | JSON mapping of label to path for additional read-only team SQLite databases (CLI: `--additional-team-dbs`) |
+| `DEFAULT_WORKSPACE_ID`                         | Default workspace ID for multi-tenant isolation (CLI: `--default-workspace-id`, default: `default`; `MCP_WORKSPACE_ID` provides a session-scoped schema-healing fallback on tool payloads) |
+| `MEMORY_JOURNAL_CONFIG`                        | Path to configuration file (`.yaml`, `.yml`, `.json`; CLI: `--config`) |
+| `LOG_LEVEL`                                    | Server log verbosity: `debug`, `info`, `notice`, `warning`, `error`, `critical` (CLI `--log-level` accepts `debug`, `info`, `warning`, `error`; default: `info`) |
+| `TRANSPORT` / `PORT` / `MCP_HOST` / `STATELESS` | Transport mode (`stdio` or `http`; CLI: `--transport`), HTTP port (`--port`, default: `3000`), bind address (`--server-host`, fallback: `HOST`, default: `localhost`), and stateless HTTP mode (`--stateless`, default: `false`) |
+| `CORS_ORIGIN` / `MCP_CORS_ORIGIN` / `MCP_RATE_LIMIT_MAX` | Allowed CORS origins (`--cors-origin`) and per-IP/minute HTTP rate limit (default: `100`) |
+| `GITHUB_TOKEN`                                 | Personal access token for GitHub integrations              |
+| `DEFAULT_PROJECT_NUMBER`                       | Default GitHub Project number for issue auto-assignment (CLI: `--default-project`) |
+| `PROJECT_REGISTRY`                             | JSON map of repo names to local paths and project numbers  |
+| `EMBEDDING_MODEL`                              | HuggingFace transformers model for semantic search (CLI: `--embedding-model`, default: `Xenova/all-MiniLM-L6-v2`) |
+| `AUTO_REBUILD_INDEX`                           | Rebuild vector search index on startup (`true`/`false`, CLI: `--auto-rebuild-index`) |
+| **Security & Tooling** | |
+| `ALLOWED_IO_ROOTS`                             | Comma-separated paths for Code Mode and IO filesystem boundaries (fail-closed in stdio; mandatory when `--transport http` is used) |
+| `MEMORY_JOURNAL_MCP_TOOL_FILTER`               | Control tool exposure (`full`, `starter`, `essential`, `codemode`, `readonly`, `-github`; CLI: `--tool-filter`, `memory-journal.config.{yaml,yml,json}` key: `"toolFilter"`. Note: `TOOL_FILTER` is a display fallback only) |
+| `CODE_MODE_MAX_RESULT_SIZE`                    | Max execution payload buffer size in Code Mode (bytes, default: `102400`) |
+| `CODEMODE_INTERNAL_FULL_ACCESS`                | Allow Code Mode to bypass tool filters internally (default: `false`) |
+| `MCP_AGENT_HEALING`                            | Enable/disable autonomous tool & parameter healing (`true`/`false`, CLI: `--no-agent-healing`) |
+| `MAX_TOOL_INPUT_ELEMENTS`                      | Max array/object elements in tool inputs (default: `25000`, `0` or `Infinity` = disabled) |
+| `MCP_AUTH_TOKEN` / `MCP_AUTH_SCOPES`           | Static Bearer authentication token (`--auth-token`, `--auth-scopes`) and comma-separated granted scopes for HTTP transport (default: `read`) |
+| `MCP_ENABLE_HSTS` / `TRUST_PROXY`              | Enable `Strict-Transport-Security` header (`--enable-hsts`) and reverse-proxy `X-Forwarded-For` trust (`--trust-proxy`) |
+| **Briefing & Context** | |
+| `BRIEFING_ENTRY_COUNT`                         | Number of granular journal entries in briefing (default: 3)|
+| `BRIEFING_SUMMARY_COUNT`                       | Number of session summaries in briefing (default: 1)       |
+| `BRIEFING_COMMIT_COUNT`                        | Number of git commits in briefing (default: 3)             |
+| `BRIEFING_IMPORTANCE_THRESHOLD`                | Minimum importance score for briefing entries (default: 0.3)|
+| `BRIEFING_INCLUDE_TEAM`                        | Include entries from the team database (default: false)    |
+| `BRIEFING_ISSUE_COUNT` / `BRIEFING_PR_COUNT` / `BRIEFING_PR_STATUS` | GitHub Issues (default: `0`), PRs (default: `0`), and PR status breakdown (default: `false`) in briefing |
+| `BRIEFING_MILESTONE_COUNT`                     | GitHub Milestones to list with titles (default: `3`)       |
+| `BRIEFING_WORKFLOW_COUNT` / `BRIEFING_WORKFLOW_STATUS` / `BRIEFING_COPILOT_REVIEWS` | CI workflow runs (default: `0`), status breakdown (default: `false`), and Copilot review state (default: `false`) |
+| `STALENESS_ACTIVE_HOURS` / `STALENESS_RECENT_DAYS` / `STALENESS_STALE_DAYS` | Thresholds for `memory://staleness` project classification (defaults: `24`h / `7`d / `30`d) |
+| `RULES_FILE_PATH` / `SKILLS_DIR_PATH` / `MEMORY_JOURNAL_WORKFLOW_SUMMARY` | Injected behavioral rules, skills boundaries, and workflow summary |
+| **OAuth (HTTP Mode)** | |
+| `OAUTH_ENABLED`                                | Enable OAuth 2.1 authentication (default: false)           |
+| `OAUTH_ISSUER` / `OAUTH_AUDIENCE` / `OAUTH_JWKS_URI` / `OAUTH_CLOCK_TOLERANCE` / `PUBLIC_ORIGIN` / `OAUTH_ALLOW_PLAINTEXT_LOOPBACK` | OAuth token verification parameters (clock tolerance default: 60s), non-loopback RFC 9728 public origin (`--public-origin`), and local dev plaintext loopback issuer flag (`--oauth-allow-plaintext-loopback`) |
+| **Telemetry & Administration** | |
+| `AUDIT_LOG_PATH` / `AUDIT_REDACT` / `AUDIT_READS` / `AUDIT_LOG_MAX_SIZE` | Path to JSONL audit log file, argument/result redaction, read-call logging, and rotation size limit (default: 10MB) |
+| `METRICS_EXPORT` / `PERSIST_METRICS` / `METRICS_PATH` / `MJ_METRICS_PORT` / `MJ_METRICS_HOST` | Prometheus export (`METRICS_EXPORT=prometheus` auto-starts the standalone metrics server on `127.0.0.1:9465` in addition to mounting `/metrics` on the HTTP transport), disk-persisted metrics (`--persist-metrics`, `--metrics-path`), and dedicated scrape port/host |
+| `AUTO_PRUNE_INTERVAL_MINUTES` / `ARCHIVE_OLDER_THAN_DAYS` / `PRUNE_OLDER_THAN_DAYS` / `HARD_DELETE_OLDER_THAN_DAYS` / `PRUNE_IMPORTANCE_THRESHOLD` / `PRUNE_DRY_RUN` / `PRUNE_EXCLUDE_TAGS` | Autonomous lifecycle pruning, archiving (interval/days default: `0` = disabled), importance threshold (default: `0.15`), dry-run (default: `false`), and exclusion tags |
+| `BACKUP_INTERVAL` / `KEEP_BACKUPS` / `VACUUM_INTERVAL` / `REBUILD_INDEX_INTERVAL` / `DIGEST_INTERVAL` | Scheduled HTTP maintenance intervals in minutes (`--backup-interval`, `--vacuum-interval`, `--rebuild-index-interval`, `--digest-interval`) and backup retention count (`--keep-backups`, default: `5`) |
+| `REPORT_INTERVAL` / `REPORT_WEBHOOK_URL` / `REPORT_WEBHOOK_AUTH` / `REPORT_CONTENT_TYPE` / `ALLOW_INSECURE_WEBHOOK_HTTP` | Scheduled HTTP reports, webhook delivery headers/content-type, and local dev HTTP webhook override |
+| `DEBUG` / `DISABLE_ISSUE_LOGGING`              | Verbose debug logging and suppression of automated runtime issue logging |
+
 ### GitHub Integration (Optional)
 
 ```bash
@@ -709,7 +636,7 @@ export GITHUB_TOKEN="your_token"              # For Projects/Issues/PRs
 
 **Scopes:** `repo`, `project`, `read:org` (org-level project discovery only)
 
-### GitHub Management Capabilities
+### Manage GitHub Seamlessly
 
 Memory Journal provides a **hybrid approach** to GitHub management:
 
@@ -720,22 +647,15 @@ Memory Journal provides a **hybrid approach** to GitHub management:
 
 **MCP Server Tools (Read + Kanban + Milestones + Issue Lifecycle):**
 
-- `get_github_issues` / `get_github_issue` - Query issues
-- `get_github_prs` / `get_github_pr` - Query pull requests
-- `get_github_context` - Full repository context
-- `get_kanban_board` / `add_kanban_item` / `move_kanban_item` / `delete_kanban_item` - **Kanban management**
-- `get_github_milestones` / `get_github_milestone` - **Milestone tracking with completion %**
-- `create_github_milestone` / `update_github_milestone` / `delete_github_milestone` - **Milestone CRUD**
-- `get_repo_insights` - **Repository traffic & analytics** (stars, clones, views, referrers, popular paths)
-- `create_github_issue_with_entry` / `close_github_issue_with_entry` - **Issue lifecycle with journal linking**
+See the **[Complete tools reference](https://github.com/neverinfamous/memory-journal-mcp/wiki/Tools)** for all supported GitHub integration capabilities, including query commands, Kanban management, milestone tracking, analytics, and issue lifecycle events.
 
 > **Why this design?** The MCP server focuses on value-added features that integrate journal entries with GitHub (Kanban views, Milestones, timeline resources, context linking). Standard GitHub mutations (create/close issues, merge PRs, manage releases) are handled directly by agents via `gh` CLI.
 
 **[Complete GitHub integration guide →](https://github.com/neverinfamous/memory-journal-mcp/wiki/Git-Integration)**
 
-### GitHub Commander Workflows
+### Automate with GitHub Commander Workflows
 
-The server natively bundles the `github-commander` agent skill (accessible via `memory://skills/github-commander`). This extends your AI assistant with 9 autonomous DevOps workflows for repository stewardship: **Issue Triage**, **Milestone Sprints**, **PR Reviews**, **Copilot Audits**, **Security Audits**, **Code Quality Audits**, **Performance Audits**, **Roadmap Kickoffs**, and **Dependency Updates**. Configure validation layers using the `PROJECT_*` environment overrides to enforce CI-matching execution locally during agent tasks!
+The server natively bundles the `memory-journal-mcp` agent skill (served via SEP-2640 and `memory://skills`). It also provides built-in `issue-commander`, `pr-commander`, and `cms-rem-supervisor` MCP workflow prompts for autonomous DevOps stewardship: **Issue Triage**, **Milestone Sprints**, **PR Reviews**, **Copilot Audits**, **Security Audits**, **Code Quality Audits**, **Performance Audits**, **Roadmap Kickoffs**, and **Dependency Updates**. These workflows enforce multi-gate validation (`lint`, `typecheck`, `test`, and security checks) locally during agent tasks.
 
 ## 🏗️ Architecture
 
@@ -745,10 +665,11 @@ The server natively bundles the `github-commander` agent skill (accessible via `
 flowchart TB
     AI["🤖 AI Agent<br/>(Cursor, Windsurf, Claude)"]
 
-    subgraph MCP["Memory Journal MCP Server"]
-        Tools["🛠️ 73 Tools"]
-        Resources["📡 46 Resources"]
-        Prompts["💬 19 Prompts"]
+    subgraph MCP["MCP Server Capabilities"]
+        direction LR
+        Tools["🛠️ MCP Tools"]
+        Resources["📡 Resources"]
+        Prompts["💬 Prompts"]
     end
 
     subgraph Storage["Persistence Layer"]
@@ -775,8 +696,7 @@ flowchart TB
 ┌─────────────────────────────────────────────────────────────┐
 │ MCP Server Layer (TypeScript)                               │
 │  ┌─────────────────┐  ┌─────────────────┐  ┌─────────────┐  │
-│  │ Tools (73)      │  │ Resources (47)  │  │ Prompts (19)│  │
-│  │ with Annotations│  │ with Annotations│  │             │  │
+│  │ Tools            │  │ Resources       │  │ Prompts       │  │
 │  └─────────────────┘  └─────────────────┘  └─────────────┘  │
 ├─────────────────────────────────────────────────────────────┤
 │ Native SQLite Engine                                        │
@@ -805,41 +725,44 @@ flowchart TB
 
 ### Performance Benchmarks
 
-Memory Journal is designed for extremely low overhead during AI task execution. We include a `vitest bench` suite to maintain these baseline guarantees:
+Memory Journal is designed for extremely low overhead during AI task execution. We include a `vitest bench` suite across database, vector search, and MCP server routines to maintain these baseline guarantees:
 
-- **Database Reads**: Operations execute in fractions of a millisecond. `calculateImportance` is ~13-14x faster than retrieving 50 recent entries.
-- **Vector Search Engine**: Both search (~140-220 ops/sec) and indexing (~1600-1900+ ops/sec) are high-throughput via `sqlite-vec` with SQL-native KNN queries.
-- **Core MCP Routines**: `getTools` uses cached O(1) dispatch (~4800-7000x faster than `get_recent_entries`). `create_entry` and `search_entries` execute through the full MCP layer with sub-millisecond overhead.
+- **Database Operations (`sqlite-adapter.bench.ts`)**: `calculateImportance` runs at **~51,600 ops/sec** (~0.03ms mean, ~27x faster than retrieving 50 recent entries) via a 256-entry LRU prepared statement cache. `getRecentEntries (limit 50)` executes at **~1,870 ops/sec** (~0.63ms mean), `updateEntry` at **~2,380 ops/sec** (~0.79ms mean), `createEntry` at **~1,060 ops/sec** (~1.69ms mean), and `searchEntries` (FTS5 BM25 + batch importance hydration) at **~176 ops/sec** (~6.2ms mean).
+- **Vector Search Engine (`vector-search.bench.ts`)**: Both k-NN similarity search (**~1,050 ops/sec**, ~1.8ms mean with batch entry hydration) and vector indexing (**~4,220 ops/sec**, ~0.41ms mean) are high-throughput via `sqlite-vec` (`vec0` with `chunk_size=256`).
+- **Core MCP Routines (`mcp-server.bench.ts`)**: `getTools` uses cached O(1) dispatch (**~7.2M–9.4M ops/sec**, ~0.0001ms). Full end-to-end `callTool` invocations (including interceptor, token estimation, and project registry resolution) run at **~1,775 ops/sec** (~0.65ms) for `get_recent_entries`, **~205 ops/sec** (~5.4ms) for `search_entries`, and **~800 ops/sec** (~2.4ms) for `create_entry`.
 
 To run the benchmarking suite locally:
 
 ```bash
-npm run bench
+pnpm run bench
 ```
 
 ### Testing
 
 Extensively tested across two frameworks:
 
-| Suite                     | Command            | Covers                                                                          |
-| ------------------------- | ------------------ | ------------------------------------------------------------------------------- |
-| Vitest (unit/integration) | `npm test`         | Database, tools, resources, handlers, security, GitHub, vector search, codemode |
-| Playwright (e2e)          | `npm run test:e2e` | HTTP/SSE transport, auth, sessions, CORS, security headers, scheduler           |
+| Suite                     | Command             | Covers                                                                          |
+| ------------------------- | ------------------- | ------------------------------------------------------------------------------- |
+| Vitest (unit/integration) | `pnpm test`         | Extensive Vitest unit and integration suite with strict quality gates (database, tools, resources, handlers, security, GitHub, vector search, codemode) |
+| Playwright (e2e)          | `pnpm run test:e2e` | HTTP/SSE transport, auth, sessions, CORS, security headers, scheduler           |
 
 ```bash
-npm test          # Unit + integration tests
-npm run test:e2e  # End-to-end HTTP/SSE transport tests
+pnpm test          # Unit + integration tests
+pnpm run test:e2e  # End-to-end HTTP/SSE transport tests
 ```
 
 ### Security
 
+> **Note**: When updating schemas or validation logic, please refer to the `/zod` skill for best practices on Standard Schema and Safe Parsing.
+
 - **Deterministic error handling** - Every tool returns structured `{success, error, code, category, suggestion, recoverable}` responses with actionable context — no raw exceptions, no silent failures, no misleading messages
 - **Local-first** - All data stored locally, no external API calls (except optional GitHub)
-- **Input validation** - Zod schemas, content size limits, SQL injection prevention
-- **Path traversal protection** - Backup filenames validated
-- **MCP 2025-03-26 annotations** - Behavioral hints (`readOnlyHint`, `destructiveHint`, etc.)
-- **HTTP transport hardening** - 7 security headers, configurable multi-origin CORS, 1MB body limit, built-in rate limiting (100 req/min), server timeouts, HSTS (opt-in), 30-min session timeout, 404 handler, cross-protocol guard
-- **Token scrubbing** - GitHub tokens and credentials automatically redacted from error logs
+- **Input validation** - Zod schemas, content size limits, SQL injection prevention, and `<untrusted_remote_content>` prompt-injection boundary tagging
+- **Path traversal & SSRF protection** - `ALLOWED_IO_ROOTS` sandbox containment with URL-decode/symlink verification, backup path validation, and outbound webhook DNS/IP SSRF blocking
+- **Multi-tenant & filter enforcement** - End-to-end `workspace_id` isolation across SQLite and Vector search, plus execution-layer `--tool-filter` enforcement across `tools/call`, Code Mode (`mj.*`), and fallback handlers
+- **MCP 2025-11-25 annotations & icons** - Behavioral hints (`readOnlyHint`, `destructiveHint`, etc.) and capability icons
+- **HTTP transport hardening** - OAuth 2.1 `tokenClaims` propagation, principal-bound stateful sessions (`100` max active sessions), comprehensive security headers, configurable multi-origin CORS, 1MB body/stream limit, built-in per-subject/IP rate limiting (100 req/min), server timeouts, HSTS (opt-in), 30-min session timeout, and localhost-bound metrics (`METRICS_EXPORT=prometheus` automatically starts the standalone metrics server on `127.0.0.1:9465`, customizable via `MJ_METRICS_PORT` and `MJ_METRICS_HOST`, in addition to mounting `/metrics` on the HTTP transport)
+- **Token scrubbing** - GitHub tokens and credentials automatically redacted from error and audit logs
 
 ### Data & Privacy
 
@@ -853,8 +776,8 @@ npm run test:e2e  # End-to-end HTTP/SSE transport tests
 ## 📚 Documentation & Resources
 
 - **[GitHub Wiki](https://github.com/neverinfamous/memory-journal-mcp/wiki)** - Complete documentation
-- **[Copilot Setup Guide](docs/copilot-setup.md)** - Cross-agent memory bridge between IDE agents and GitHub Copilot
-- **[Deployment Guide](docs/deployment.md)** - CI/CD pipeline, environments, and version bump checklist
+- **[Copilot Setup Guide](https://github.com/neverinfamous/memory-journal-mcp/wiki)** - Cross-agent memory bridge between IDE agents and GitHub Copilot
+- **[Deployment Guide](https://github.com/neverinfamous/memory-journal-mcp/wiki/Deployment)** - CI/CD pipeline, environments, and version bump checklist
 - **[Docker Hub](https://hub.docker.com/r/writenotenow/memory-journal-mcp)** - Container images
 - **[npm Package](https://www.npmjs.com/package/memory-journal-mcp)** - Node.js distribution
 - **[Issues](https://github.com/neverinfamous/memory-journal-mcp/issues)** - Bug reports & feature requests
@@ -867,4 +790,6 @@ MIT License - See [LICENSE](LICENSE) file for details.
 
 ## 🤝 Contributing
 
-Built by developers, for developers. PRs welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+Built by developers, for developers. PRs welcome! Ensure all unit and E2E tests, linting, and typechecks pass. See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+_Upgrading from an earlier version?_ Your existing SQLite database is automatically migrated on startup.