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phren MCP server

MCP server that indexes your personal phren and exposes it to AI agents via full-text search.

On startup it walks your phren directory, reads all .md files, and builds an in-memory SQLite FTS5 index.

Periodic remote checks are off by default. Enable them with phren config pull-interval 60 to check shared Git stores every minute while running, coordinated across MCP clients using the same store. Changed refs are fetched and applied only as clean fast-forwards; dirty or diverged stores are deferred. Pulled changes refresh the index and existing managed skill/instruction mirrors. Configure this machine with phren config pull-interval 600 (ten minutes) or phren config pull-interval off. Periodic checks are disabled for project-local stores and the manual preset; existing lifecycle hooks are configured separately.

Public surface: 76 MCP implementation tools across 16 catalog modules (search, tasks, findings, notes, memory, data, graph, sessions, ops/review, skills, hooks, config, extraction).

Notable shipped capabilities:

• finding lifecycle tools: supersede_finding, retract_finding, resolve_contradiction, get_contradictions
• finding provenance: add_finding.source (human|agent|hook|extract|consolidation|unknown)
• lightweight daily notes: CRUD in <project>/notes/YYYY-MM-DD.md, explicit search, and promotion to findings without automatic prompt injection
• cross-session continuity: task checkpoints + session_history
• finding impact scoring from injected-context outcomes
• skill registry behavior: scope precedence, alias-collision handling, visibility gating, generated skill-manifest.json
• lifecycle penalties: superseded 0.25×, retracted 0.1×, contradicted 0.4× confidence in retrieval
• inactive findings stripped from FTS index (superseded/retracted findings cannot appear in search)
• auto-tagging: findings without type tags are inferred from content at write time
• session context diff: session_start reports new findings since last session
• decay resistance: confirmed findings decay 3× slower when repeatedly useful

Install

npx @phren/cli init

This sets up phren without needing sudo or a global install. On Windows, use npm install -g @phren/cli if npx isn't available.

Or add manually to Claude Code:

claude mcp add phren -- phren ~/.phren

Environment variables

Variable	Default	Description
PHREN_PATH	~/.phren	Path to your phren instance
PHREN_PROFILE	(none)	Active profile name. When unset, phren uses machines.yaml when available and otherwise falls back to an unscoped view
PHREN_PULL_INTERVAL_SECONDS	0 (off)	Overrides the machine-local pull interval. Whole seconds from 30–86400, or 0/off to disable periodic MCP checks.
PHREN_ACTOR	OS user / env	Actor identity used in governance/audit RBAC checks

Tools

See docs/api-reference.md for the full API reference.

Integration model

• Claude: full native lifecycle hooks (SessionStart, UserPromptSubmit, Stop, PostToolUse) + MCP
• Copilot CLI / Cursor / Codex: MCP + generated hook config + session wrapper binaries

Governance and security highlights

• RBAC uses .config/access-control.json and .runtime/access-control.local.json
• Web UI binds loopback-only, uses per-run auth token, enforces CSRF for mutations, and sets CSP headers
• Telemetry is opt-in only (phren config telemetry on) and stored locally in .runtime/telemetry.json

search_knowledge

Full-text search across all indexed markdown files with synonym expansion.

query: string              - FTS5 query (supports AND, OR, NOT, "phrase matching")
limit?: number             - Max results, 1-20, default 5
type?: string              - Filter: "claude", "findings", "reference", "summary", "task", "skill"
project?: string           - Filter to a specific project
tag?: string               - Filter findings by type tag: decision, pitfall, pattern, tradeoff, architecture, bug
since?: string             - Filter findings by date: "7d", "30d", "YYYY-MM", "YYYY-MM-DD"
status?: string            - Filter by lifecycle status: active, superseded, contradicted, stale, invalid_citation, retracted
include_history?: boolean  - Include superseded/retracted findings (default false)
synthesize?: boolean       - Generate a synthesis paragraph from top results using an LLM

get_project_summary

Returns a project's summary.md content, path to its AGENTS.md, and a list of indexed files.

name: string      - Project name (e.g. "my-app", "backend")

list_projects

Lists all projects in the active profile with a brief description and which docs exist.

No parameters.

How it works

1. Reads PHREN_PATH (or defaults to ~/.phren)
2. Resolves the active profile from PHREN_PROFILE, or from machines.yaml when the env var is unset
3. If no active profile can be resolved yet, falls back to an unscoped view of top-level project directories
4. Walks each project directory, reads .md files, classifies them by filename
5. Builds an in-memory SQLite FTS5 index with Porter stemming
6. Serves tools over stdio using the MCP protocol

File types are derived from filenames and directories: AGENTS.md -> "claude", summary.md -> "summary", FINDINGS.md -> "findings", tasks.md -> "task", files under notes/ -> "notes", files under reference/ -> "reference", files under skills/ -> "skill".

Development

cd ~/phren
npm install
npm run build    # Compile TypeScript
npm run dev      # Run with tsx (hot reload)
npm test         # Run all tests