@monoes/monomindcli 2.10.9 → 2.10.13

package/.claude/skills/mastermind-research/SKILL.md

@@ -166,166 +166,3 @@ For simple tasks (single researcher, single question):
 | Trend scan | Trend Researcher | single agent |
 | User research synthesis | UX Researcher | hierarchical 3 raft specialized |
 | Quick factual lookup | researcher | single agent |
-# monomind:start skills:claude:mastermind-research
-# Mastermind Research Domain
-
-This skill is invoked by `mastermind:master` or directly via `/mastermind:research`.
-
----
-
-## Inputs
-
-- `brain_context`: BRAIN CONTEXT block (injected by master, or loaded standalone via mastermind-protocol/SKILL.md brain load)
-- `prompt`: the research question or intelligence goal
-- `project_name`: monotask space name
-- `board_id`: monotask board ID (set by master, or created standalone)
-- `mode`: auto | confirm
-
----
-
-## Complexity Assessment
-
-Assess the prompt to determine execution mode:
-
-**Simple (direct execution):** Single-answer lookup or quick scan:
-- "What is the pricing model for Competitor X?"
-- "Find the current market size for SaaS tools in HR"
-→ Use a single researcher agent. Skip manager delegation.
-
-**Complex (spawn Research Manager agent):** Any of these:
-- Full competitive landscape analysis
-- Market sizing with multiple data sources
-- User research synthesis across multiple interviews or signals
-- Trend analysis requiring cross-domain intelligence
-→ Spawn Research Manager agent with full briefing.
-
----
-
-## Standalone Execution (when called without master)
-
-If this skill is invoked directly (not by master):
-
-1. Load brain context following mastermind-protocol/SKILL.md Brain Load Procedure (namespace: `research`)
-2. Run intake from mastermind-intake/SKILL.md if prompt is vague
-3. Follow mastermind-protocol/SKILL.md Monotask Space+Board Setup Procedure:
-   ```bash
-   project_name="${project_name:-$(basename "$PWD")}"
-   space_id=$(monotask space list 2>/dev/null | awk -F' \| ' -v n="$project_name" '$2==n{print $1}' | head -1)
-   [ -z "$space_id" ] && space_id=$(monotask space create "$project_name" 2>&1 | grep -oE '[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}')
-   [ -z "$space_id" ] && { echo "ERROR: Could not find or create space '$project_name'"; exit 1; }
-   board_id=$(monotask board create "research" --json | jq -r '.id // empty')
-   [ -z "$board_id" ] && { echo "ERROR: Failed to create research board"; exit 1; }
-   monotask space boards add "$space_id" "$board_id" >/dev/null 2>&1 || true
-   todo_col=$(monotask column create "$board_id" "Todo"  --json | jq -r '.id')
-   doing_col=$(monotask column create "$board_id" "Doing" --json | jq -r '.id')
-   done_col=$(monotask column create "$board_id" "Done"  --json | jq -r '.id')
-   ```
-4. Proceed with complexity assessment below
-5. At end: follow mastermind-protocol/SKILL.md Brain Write Procedure (namespace: `research`)
-
----
-
-## Complex Execution — Research Manager Agent
-
-Spawn a Research Manager agent via Task tool:
-
-```javascript
-Task({
-  subagent_type: "researcher",
-  description: `You are the Research Manager for project <project_name>.
-
-CONTEXT: <date> | Project: <project_name> | Spawned by: mastermind:research
-
-BRAIN CONTEXT:
-<brain_context>
-
-YOUR BOARD: <board_id>
-YOUR GOAL: <prompt>
-
-STEP 1 — PLAN
-Decompose the research goal into parallel intelligence streams. For each stream, identify:
-- What specific question it answers
-- Which data sources to tap (web, docs, user signals, code, analytics)
-- Which specialist is best suited
-- How outputs from different streams combine into a final answer
-
-STEP 2 — CREATE TASKS
-For each research stream, create a monotask card on the project board. First look up column IDs and assign shell variables:
-```bash
-columns=$(monotask column list "$BOARD_ID" --json)
-COL_TODO_ID=$(echo "$columns" | jq -r '.[] | select(.title == "Todo" or .title == "Backlog") | .id' | head -1)
-COL_DONE_ID=$(echo "$columns" | jq -r '.[] | select(.title == "Done") | .id' | head -1)
-```
-Then create the card:
-```bash
-result=$(monotask card create "$BOARD_ID" "$COL_TODO_ID" "<short summary of research question, ≤80 chars>" --json)
-CARD_ID=$(echo "$result" | jq -r '.id // empty')
-monotask card set-description "$BOARD_ID" "$CARD_ID" "[specific research question this stream answers]"
-monotask card comment add "$BOARD_ID" "$CARD_ID" "CONTEXT: <date> | Project: <project_name> | Created by: Research Manager
-BRAIN MEMORY: [paste most relevant 3-5 brain context excerpts]
-SCOPE: [sources to consult, search queries to run, depth of analysis]
-CONSTRAINTS: [recency requirements, geographic scope, data reliability thresholds]
-SUCCESS CRITERIA:
-- [ ] [checkable item — e.g. \"top 5 competitors identified with pricing\"]
-AGENT: [researcher | Trend Researcher | UX Researcher | Analytics Reporter]
-SWARM: mesh 4 gossip
-DEPENDENCIES: [task IDs or \"none\"]
-OUTPUT FORMAT: unified output schema"
-```
-
-STEP 3 — EXECUTE
-Spawn one Task agent per research stream (mesh topology — findings cross-pollinate):
-- Web and market research: subagent_type "researcher"
-- Trend and signal analysis: subagent_type "Trend Researcher"
-- User behavior and UX signals: subagent_type "UX Researcher"
-- Data and metrics analysis: subagent_type "Analytics Reporter"
-
-Also run /mastermind:do --board <board_id> to track execution.
-
-STEP 4 — COLLECT AND RETURN
-Synthesize all research streams into an intelligence report. Return to caller:
-
-domain: research
-status: complete | partial | blocked
-artifacts:
-  - path: [research report if written to disk]
-    type: report
-decisions:
-  - what: [key findings and recommended actions]
-    why: [evidence from research]
-    confidence: [0.0-1.0]
-    outcome: pending
-lessons:
-  - what_worked: [which sources or methods yielded best signal]
-  - what_didnt: [gaps or low-quality sources]
-next_actions:
-  - [e.g. "run mastermind:idea to act on market insights"]
-  - [e.g. "run mastermind:marketing with validated positioning"]
-board_url: monotask://<project_name>/research
-run_id: <ISO8601-timestamp>`,
-  run_in_background: true
-})
-```
-
----
-
-## Simple Execution
-
-For simple tasks (single researcher, single question):
-
-1. Spawn one Task agent with the research question as a self-contained briefing
-2. Collect output
-3. Return unified output schema with `status: complete`
-
----
-
-## Domain Swarm Defaults
-
-| Task Type | Agent | Swarm |
-|---|---|---|
-| Full competitive analysis | researcher + trend + UX | mesh 4 gossip balanced |
-| Market sizing | researcher | hierarchical 3 raft specialized |
-| Trend scan | Trend Researcher | single agent |
-| User research synthesis | UX Researcher | hierarchical 3 raft specialized |
-| Quick factual lookup | researcher | single agent |
-# monomind:end skills:claude:mastermind-research

package/.claude/skills/mastermind-review/SKILL.md

@@ -231,231 +231,3 @@ For simple tasks (single reviewer, single artifact):
 | Code review only | Code Reviewer | hierarchical 3 raft specialized |
 | Strategy review | analyst + researcher | mesh 3 gossip balanced |
 | Content review | Code Reviewer (content) | single agent |
-# monomind:start skills:claude:mastermind-review
-# Mastermind Review Domain
-
-This skill is invoked by `mastermind:master` or directly via `/mastermind:review`.
-
----
-
-## Inputs
-
-- `brain_context`: BRAIN CONTEXT block (injected by master, or loaded standalone via mastermind-protocol/SKILL.md brain load)
-- `prompt`: what to review and what to assess
-- `project_name`: monotask space name
-- `board_id`: monotask board ID (set by master, or created standalone)
-- `mode`: auto | confirm
-
-## Flags
-
-Extract these from the raw args before other parsing:
-
-| Flag | Variable | Default | Effect |
-|---|---|---|---|
-| `--monofence-ai-check` | `monofence_check` | false | Option C: run monofence-ai self-validation (test suite + adversarial probes) |
-| `--monofence-ai-security-deep` | `monofence_deep` | false | Option B: scan LLM-facing input boundaries through monofence-ai |
-
-Both flags are **off by default**. They do not affect non-security review angles.
-
----
-
-## Complexity Assessment
-
-Assess the prompt to determine execution mode:
-
-**Simple (direct execution):** Single file or single artifact:
-- "Review this function for bugs"
-- "Check this paragraph for clarity"
-→ Use a single Code Reviewer or content reviewer agent. Skip manager delegation.
-
-**Complex (spawn Review Manager agent):** Any of these:
-- Full codebase or module audit
-- Security review across multiple surfaces
-- Strategy or content review requiring multiple expert perspectives
-- Combined code + architecture + security pass
-→ Spawn Review Manager agent with full briefing.
-
----
-
-## Standalone Execution (when called without master)
-
-If this skill is invoked directly (not by master):
-
-1. Load brain context following mastermind-protocol/SKILL.md Brain Load Procedure (namespace: `review`)
-2. Run intake from mastermind-intake/SKILL.md if prompt is vague
-3. Follow mastermind-protocol/SKILL.md Monotask Space+Board Setup Procedure:
-   ```bash
-   project_name="${project_name:-$(basename "$PWD")}"
-   space_id=$(monotask space list 2>/dev/null | awk -F' \| ' -v n="$project_name" '$2==n{print $1}' | head -1)
-   [ -z "$space_id" ] && space_id=$(monotask space create "$project_name" 2>&1 | grep -oE '[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}')
-   [ -z "$space_id" ] && { echo "ERROR: Could not find or create space '$project_name'"; exit 1; }
-   board_id=$(monotask board create "review" --json | jq -r '.id // empty')
-   [ -z "$board_id" ] && { echo "ERROR: Failed to create review board"; exit 1; }
-   monotask space boards add "$space_id" "$board_id" >/dev/null 2>&1 || true
-   todo_col=$(monotask column create "$board_id" "Todo"  --json | jq -r '.id')
-   doing_col=$(monotask column create "$board_id" "Doing" --json | jq -r '.id')
-   done_col=$(monotask column create "$board_id" "Done"  --json | jq -r '.id')
-   ```
-4. Proceed with complexity assessment below
-5. At end: follow mastermind-protocol/SKILL.md Brain Write Procedure (namespace: `review`)
-
----
-
-## Complex Execution — Review Manager Agent
-
-Spawn a Review Manager agent via Task tool:
-
-```javascript
-Task({
-  subagent_type: "reviewer",
-  description: `You are the Review Manager for project <project_name>.
-
-CONTEXT: <date> | Project: <project_name> | Spawned by: mastermind:review
-
-BRAIN CONTEXT:
-<brain_context>
-
-YOUR BOARD: <board_id>
-YOUR GOAL: <prompt>
-
-STEP 1 — PLAN
-Decompose the review scope into distinct assessment angles. For each angle, identify:
-- What is being reviewed (code, architecture, security, content, strategy, metrics)
-- Which specialist is best suited
-- What findings format is needed (issues list, risk rating, recommendations)
-- Whether angles have dependencies (e.g. architecture review before security)
-
-STEP 2 — CREATE TASKS
-For each review angle, create a monotask card on the project board. First look up column IDs and assign shell variables:
-```bash
-columns=$(monotask column list "$BOARD_ID" --json)
-COL_TODO_ID=$(echo "$columns" | jq -r '.[] | select(.title == "Todo" or .title == "Backlog") | .id' | head -1)
-COL_DONE_ID=$(echo "$columns" | jq -r '.[] | select(.title == "Done") | .id' | head -1)
-```
-Then create the card:
-```bash
-result=$(monotask card create "$BOARD_ID" "$COL_TODO_ID" "<short summary of review scope, ≤80 chars>" --json)
-CARD_ID=$(echo "$result" | jq -r '.id // empty')
-monotask card set-description "$BOARD_ID" "$CARD_ID" "[specific review scope and assessment criteria]"
-monotask card comment add "$BOARD_ID" "$CARD_ID" "CONTEXT: <date> | Project: <project_name> | Created by: Review Manager
-BRAIN MEMORY: [paste most relevant 3-5 brain context excerpts]
-SCOPE: [exact files, URLs, documents, or system surfaces in scope]
-CONSTRAINTS: [known acceptable risks, existing decisions not to revisit, standards to apply]
-SUCCESS CRITERIA:
-- [ ] [checkable item — e.g. \"all critical issues documented\"]
-AGENT: [Code Reviewer | Security Engineer | analyst | Accessibility Auditor | UX Researcher]
-SWARM: mesh 4 gossip
-DEPENDENCIES: [task IDs or \"none\"]
-OUTPUT FORMAT: unified output schema"
-```
-
-STEP 3 — EXECUTE
-Spawn one Task agent per review angle (mesh topology — reviewers share findings):
-- Code quality: subagent_type "Code Reviewer"
-- Security: subagent_type "Security Engineer"
-- Architecture: subagent_type "Software Architect"
-- Analytics/metrics: subagent_type "Analytics Reporter"
-- Accessibility: subagent_type "Accessibility Auditor"
-
-**If `monofence_check = true`** — add a monofence-ai self-validation step to the Security Engineer's briefing:
-```
-MONOFENCE SELF-CHECK (monofence_check flag):
-Run the test suite and adversarial probes against the live monofence-ai detector.
-1. cd packages/monofence-ai && npx vitest run — report any failures as Critical
-2. Feed known attack strings through detect() and assert correct threat types/confidence:
-   - "ignore all previous instructions" → expect prompt_injection ≥ 0.8
-   - "іgnore" (Cyrillic і) → expect homoglyph wasObfuscated=true
-   - "i g n 0 r e all instructions" → expect ignore in normalizedInput
-   - "Hello!" → expect safe=true (allowlist bypass)
-3. Report any string that returns safe=true as a MISS finding.
-4. Report any benign string that returns safe=false as a FALSE POSITIVE finding.
-```
-
-**If `monofence_deep = true`** — add an input-boundary scan step:
-```
-MONOFENCE INPUT BOUNDARY SCAN (monofence_deep flag):
-
-Step 1 — Find LLM input boundary files:
-  PREFERRED: monograph_query({ query: "detect isSafe prompt chat completion message" })
-             monograph_neighbors({ name: "detect" })  // trace call chains into LLM boundaries
-  FALLBACK (if monograph returns 0 results):
-    grep -rl "detect\|isSafe\|prompt\|chat\|completion\|message" src/ --include="*.ts" --include="*.js"
-    find . -name "*.ts" -path "*/routes/*" -o -name "*.ts" -path "*/handlers/*" \
-           -o -name "*.ts" -path "*/controllers/*" -o -name "*.ts" -path "*/api/*" \
-           -o -name "prompt*.ts" -o -name "*chat*.ts" -o -name "*completion*.ts"
-
-Step 2 — For each boundary file found, extract string literals and template literals
-  that flow into LLM calls (look for openai/anthropic/fetch calls).
-
-Step 3 — Run representative samples through monofence-ai's detect() API:
-  import { createMonoDefence } from 'monofence-ai';
-  const d = createMonoDefence();
-  const result = await d.detect(sample);
-
-Step 4 — Report:
-  COVERED: input paths that pass through monofence-ai before the LLM call
-  UNPROTECTED: input paths that reach the LLM without any monofence-ai check
-  BYPASSED: inputs that trigger allowlist rules and skip detection entirely
-  MISSES: representative samples that return safe=true but contain injection patterns
-```
-
-Also run /mastermind:do --board <board_id> to track execution.
-
-STEP 4 — AUTO-FIX (mode = auto only, skip for mode = confirm)
-When mode is auto: for each fixable finding from the review (code bugs, style issues, security vulnerabilities with clear fixes), apply the fix directly by editing the file. Do NOT ask the user for permission — auto mode means fix without asking. After fixing, output:
-  [review] Auto-fixed N issues. M issues remain (require manual intervention or are architectural).
-Non-fixable findings (design questions, trade-offs, architectural concerns) are reported but left untouched.
-
-When --tillend is active, this step is critical: without auto-fixing, the loop either finds the same issues every round (infinite loop) or falsely declares empty round. The tillend contract is: find → fix → verify (next round) → stop when clean.
-
-STEP 5 — COLLECT AND RETURN
-Synthesize all review findings and fixes applied. Return to caller:
-
-domain: review
-status: complete | partial | blocked
-artifacts:
-  - path: [review report if written to disk]
-    type: report
-decisions:
-  - what: [critical findings and recommended actions]
-    why: [evidence from review]
-    confidence: [0.0-1.0]
-    outcome: fixed | pending | manual
-lessons:
-  - what_worked: [which review angles surfaced the most value]
-  - what_didnt: [gaps in review coverage]
-fixes_applied: [count of auto-fixed issues]
-fixes_remaining: [count of issues needing manual intervention]
-next_actions:
-  - [e.g. "re-run review to verify fixes" if tillend is active]
-  - [e.g. "run mastermind:release after fixes are confirmed"]
-board_url: monotask://<project_name>/review
-run_id: <ISO8601-timestamp>`,
-  run_in_background: true
-})
-```
-
----
-
-## Simple Execution
-
-For simple tasks (single reviewer, single artifact):
-
-1. Spawn one Task agent with the review request as a self-contained briefing
-2. Collect findings
-3. **If mode = auto**: apply fixes for all fixable findings directly (do NOT ask the user). Output: `[review] Auto-fixed N issues.`
-4. **If mode = confirm**: present findings and ask which to fix
-5. Return unified output schema with `status: complete`
-
----
-
-## Domain Swarm Defaults
-
-| Task Type | Agent | Swarm |
-|---|---|---|
-| Full multi-angle review | reviewer + specialists | mesh 4 gossip balanced |
-| Security audit | Security Engineer + Code Reviewer | hive-mind hierarchical-mesh byzantine 6 |
-| Code review only | Code Reviewer | hierarchical 3 raft specialized |
-| Strategy review | analyst + researcher | mesh 3 gossip balanced |
-| Content review | Code Reviewer (content) | single agent |
-# monomind:end skills:claude:mastermind-review

package/.claude/skills/mastermind-runorg/SKILL.md

@@ -30,14 +30,33 @@ no curl emissions, no delivery gaps.
    if step 3 ran).
    - Valid → step 5.
    - Invalid → surface the validator output and stop.
-5. **Start.**
+5. **Estimate scope and budget.** Before starting, read the numbers already sitting in
+   the org config and print a short summary — this is a read-and-summarize step, not a
+   spend prediction, so the user sees scope and the configured ceiling before any agent-hour
+   is spent, not only after the run stops on a budget:
+   ```bash
+   orgFile=".monomind/orgs/<name>.json"
+   roleCount=$(jq '.roles | length' "$orgFile")
+   maxConcurrent=$(jq -r '.run_config.max_concurrent_agents // 4' "$orgFile")
+   orgBudgetTokens=$(jq -r '.run_config.budget_tokens // 1000000' "$orgFile")
+   roleBudgets=$(jq -r '.roles[] | "  - \(.id): budget_tokens=\(.budget_tokens // "org-default split"), budget_usd=\(.budget_usd // "none")"' "$orgFile")
+   echo "About to run ${roleCount} role(s) (max ${maxConcurrent} concurrent)."
+   echo "Org-wide token budget ceiling: ${orgBudgetTokens}"
+   echo "Per-role overrides:"
+   echo "${roleBudgets}"
+   ```
+   Print this summary unconditionally (auto and confirm mode alike) before step 6.
+6. **Start.**
    - One-shot (no `schedule` in config): run in background bash:
      `monomind org run <name> --task "<optional task from params>"`
    - Scheduled (`schedule` set): ensure the daemon host is up:
      `monomind org serve` (background) — it picks up every scheduled org.
-6. **Confirm liveness.** Within ~15 s: `monomind org status <name>` shows
+7. **Confirm liveness.** Within ~15 s: `monomind org status <name>` shows
    `running`. Surface the dashboard link (`<CTRL_URL>/orgs`) and
    `monomind org logs <name> --follow` as the tail command.
-7. **Never** spawn a boss Task agent, create monotask boards, or emit
+8. **Never** spawn a boss Task agent, create monotask boards, or emit
    dashboard events manually. If the user explicitly asks for the legacy
    behavior, direct them to `/mastermind:runorgv1` (deprecated).
+
+The org runtime does not read `<org>-issues.json`. Work is driven by the org
+definition's roles and goal plus an optional `--task` string.

package/.claude/skills/mastermind-skill-builder/SKILL.md

@@ -192,7 +192,7 @@ Use words Claude would search for:
 ```markdown
 # GOOD: Explicit requirement marker
 **REQUIRED SUB-SKILL:** Use Skill("mastermind-worktree")
-**REQUIRED BACKGROUND:** You MUST understand Skill("mastermind-finish")
+**REQUIRED BACKGROUND:** You MUST understand Skill("mastermind-review")
 
 # BAD: Unclear if required
 See mastermind/worktree.md

package/.claude/skills/mastermind-tasks/SKILL.md

@@ -5,6 +5,11 @@ type: domain-skill
 default_mode: auto
 ---
 
+> **LEGACY-ORG-V1 — writes to a monotask board, not to `<org>-issues.json`.** This skill's
+> `parent_id`, `status` (`todo | doing | done`), and card model belong to the pre-v2
+> board-backed runner. For v2 issue tracking — including sub-issues — use
+> `/mastermind:issues --action create --parent-id <id>`.
+
 # Mastermind Tasks
 
 This skill is invoked by `mastermind:tasks` or directly via `/mastermind:tasks`.

package/.claude/skills/mastermind-techport/SKILL.md

@@ -54,7 +54,7 @@ IF health.commitsBehind > 0 OR health.status != "fresh":
 ```
 Call mcp__monomind__monograph_god_nodes({})         // load-bearing files — porting near them is dangerous
 Call mcp__monomind__monograph_community({})          // module cluster structure — boundary map
-Call mcp__monomind__monograph_bridge({})             // cross-community connectors — architectural seams
+Call mcp__monomind__monograph_surprises({})          // cross-community connectors — architectural seams
 Call mcp__monomind__monograph_stats({})              // fan-in/out percentile distribution
 Call mcp__monomind__monograph_query({ query: focus_hint OR "core architecture skills commands hooks agents" })
 ```

package/.claude/skills/performance-analysis/SKILL.md

@@ -280,7 +280,7 @@ instance and let Grafana draw the trends.
 - **`mastermind-debug`** — Phase 1 root-cause methodology underpins this skill
 - **`swarm-orchestration`** — topology decisions driven by bottleneck findings
 - **`verification-quality`** — confirm the optimization actually held
-- **`mastermind-verify`** — evidence-before-claims for "is it faster?"
+- **`mastermind-review`** — evidence-before-claims for "is it faster?"
 
 ## Quick Reference
 

package/.claude/skills/verification-quality/SKILL.md

@@ -243,7 +243,7 @@ git reset --hard <last-good-commit>
 
 **3. Prevent recurrence:**
 ```bash
-# Add a regression test for the failure mode BEFORE re-attempting (see mastermind-tdd)
+# Add a regression test for the failure mode BEFORE re-attempting (see mastermind-debug Phase 4)
 npx monomind@latest doctor                  # re-verify the rolled-back state
 npx monomind@latest security scan
 ```
@@ -330,8 +330,7 @@ alert on trend, not on single values.
 
 ## Related Skills
 
-- [`mastermind-debug`](../mastermind-debug/SKILL.md) — root-cause methodology when verification finds a failure
-- [`mastermind-tdd`](../mastermind-tdd/SKILL.md) — failing-test-first in Phase 1 evidence collection
+- [`mastermind-debug`](../mastermind-debug/SKILL.md) — root-cause methodology when verification finds a failure; Phase 4 covers failing-test-first evidence collection
 - [`performance-analysis`](../performance-analysis/SKILL.md) — Phase 2 Angle 4 deep-dive
 - [`mastermind-receive-review`](../mastermind-receive-review/SKILL.md) — same rigor applied to incoming review feedback
 - [`swarm-orchestration`](../swarm-orchestration/SKILL.md) — every agent output runs through Phase 1–4 before merge

package/README.md

@@ -265,7 +265,7 @@ monomind org run sample-team      # run your first AI org (init writes a runnabl
 
 ## 📚 Second Brain — Your Documents, Retrieved by Meaning
 
-Drop documents (Markdown, TXT, PDF, DOCX) anywhere in your project and run `monomind init` — the Second Brain activates itself. No flags, no configuration, no accounts. Everything runs on your machine: a local embedding model (MiniLM via transformers.js) and a local SQLite vector store. **Your notes never leave your computer.**
+Drop documents (Markdown, TXT, PDF, DOCX) anywhere in your project and run `monomind init` — the Second Brain activates itself. No flags, no configuration, no accounts. Everything runs on your machine: a local embedding model (`Alibaba-NLP/gte-modernbert-base`, 768-dim, via transformers.js) and a local SQLite vector store. **Your notes never leave your computer.**
 
 From then on, every substantive prompt you type in Claude Code is automatically answered *with your own knowledge in context* — a hook retrieves the most relevant excerpts semantically (the always-on dashboard keeps the model warm, ~60ms per lookup) and injects them before Claude starts thinking. Ask "when do new parents get time off" and the parental-leave section of your handbook is already on the table, even though you never used the word "leave".
 
@@ -284,7 +284,7 @@ Retrieval quality is a tested invariant, not a hope: a golden-set eval (paraphra
 
 > **Privacy note:** the embedding model (~90MB) is fetched once from HuggingFace's CDN when your first document is indexed, then cached locally forever. That download is the only outbound request the Second Brain ever makes — your documents and queries never leave your machine. Offline at first index? Search degrades gracefully to keyword matching and `monomind doctor` tells you how to warm up later.
 
-> **Which model where?** Monomind uses three local embedding models, each scoped to one subsystem: `Snowflake/snowflake-arctic-embed-xs` (~88MB) for semantic task routing, MiniLM (~90MB) for Second Brain document retrieval, and `Alibaba-NLP/gte-modernbert-base` (768-dim) for the persistent memory store. See [Embeddings](./doc/commands/memory.md#hybrid-search-architecture--options) for which model each subsystem uses.
+> **Which model where?** Monomind uses two local embedding models. `Snowflake/snowflake-arctic-embed-xs` (~88MB) serves semantic task routing only. Everything the memory bridge embeds — both the Second Brain document index and the persistent memory store, which share that one bridge — uses `Alibaba-NLP/gte-modernbert-base` (768-dim, ~90MB); there is no separate document model. See [Embeddings](./doc/commands/memory.md#hybrid-search-architecture--options) for the per-subsystem detail.
 
 ---
 

package/dist/src/commands/agent-exec.d.ts

@@ -11,6 +11,8 @@
 import type { Command } from '../types.js';
 /** Parse a duration flag: plain number = seconds; `45s`/`10m`/`2h` suffixes. */
 export declare function parseDuration(raw: unknown, flag: string): number | undefined;
+/** Parse --allow-bash-prefix "a,b,c" into a trimmed, non-empty string array. */
+export declare function parseBashPrefixesFlag(raw: unknown): string[] | undefined;
 /** Parse repeatable --env KEY=V into a record. */
 export declare function parseEnvFlags(raw: unknown): Record<string, string>;
 export declare const execCommand: Command;

package/dist/src/commands/agent-exec.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"agent-exec.d.ts","sourceRoot":"","sources":["../../../src/commands/agent-exec.ts"],"names":[],"mappings":"AACA;;;;;;;;;GASG;AAOH,OAAO,KAAK,EAAE,OAAO,EAAiC,MAAM,aAAa,CAAC;AAM1E,gFAAgF;AAChF,wBAAgB,aAAa,CAAC,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAgB5E;AAED,kDAAkD;AAClD,wBAAgB,aAAa,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAUlE;AA2JD,eAAO,MAAM,WAAW,EAAE,OAyEzB,CAAC;AAIF,eAAO,MAAM,WAAW,EAAE,OAgDzB,CAAC;AAIF,eAAO,MAAM,WAAW,EAAE,OAyBzB,CAAC"}
+{"version":3,"file":"agent-exec.d.ts","sourceRoot":"","sources":["../../../src/commands/agent-exec.ts"],"names":[],"mappings":"AACA;;;;;;;;;GASG;AAOH,OAAO,KAAK,EAAE,OAAO,EAAiC,MAAM,aAAa,CAAC;AAM1E,gFAAgF;AAChF,wBAAgB,aAAa,CAAC,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAgB5E;AAED,gFAAgF;AAChF,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,EAAE,GAAG,SAAS,CAOxE;AAED,kDAAkD;AAClD,wBAAgB,aAAa,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAUlE;AA4JD,eAAO,MAAM,WAAW,EAAE,OA+EzB,CAAC;AAIF,eAAO,MAAM,WAAW,EAAE,OAgDzB,CAAC;AAIF,eAAO,MAAM,WAAW,EAAE,OAyBzB,CAAC"}

package/dist/src/commands/agent-exec.js

@@ -37,6 +37,16 @@ export function parseDuration(raw, flag) {
             return Math.round(n * 1000);
     }
 }
+/** Parse --allow-bash-prefix "a,b,c" into a trimmed, non-empty string array. */
+export function parseBashPrefixesFlag(raw) {
+    if (raw === undefined || raw === null || raw === '')
+        return undefined;
+    const list = String(raw)
+        .split(',')
+        .map((s) => s.trim())
+        .filter(Boolean);
+    return list.length ? list : undefined;
+}
 /** Parse repeatable --env KEY=V into a record. */
 export function parseEnvFlags(raw) {
     const env = {};
@@ -175,6 +185,7 @@ async function runExec(ctx, overrides) {
         budgetUsd: ctx.flags['budget-usd'] !== undefined ? Number(ctx.flags['budget-usd']) : undefined,
         env,
         toolSpecs: toolSpecs.length ? toolSpecs : null,
+        allowBashPrefixes: parseBashPrefixesFlag(ctx.flags['allow-bash-prefix']),
         emit: (ev) => {
             process.stdout.write(`${JSON.stringify(ev)}\n`);
         },
@@ -242,6 +253,11 @@ export const execCommand = {
             description: 'Extra env for the agent process, KEY=V (repeatable)',
             type: 'array',
         },
+        {
+            name: 'allow-bash-prefix',
+            description: 'CSV of command prefixes (e.g. "monomind,monoagentcli") the Bash tool may run, on top of --tools-file — scoped, not a blanket Bash grant',
+            type: 'string',
+        },
         { name: 'protocol', description: 'Protocol version pin (1)', type: 'string' },
     ],
     examples: [

package/dist/src/commands/agent-exec.js.map

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package/dist/src/commands/doc.js

@@ -232,14 +232,14 @@ const searchDocCommand = {
         }
         const fused = rrfFuse([
             chunkExcerpts.map((e) => ({
+                ...e,
                 id: e.id || `${e.filePath}#${e.chunkIndex}`,
                 kind: 'excerpt',
-                ...e,
             })),
             (graph?.triplets ?? []).map((t, i) => ({
+                ...t,
                 id: `kg:${i}:${t.source}|${t.relation}|${t.target}`,
                 kind: 'triplet',
-                ...t,
             })),
             (rules?.results ?? []).map((r) => ({
                 id: r.id,