@monoes/monomindcli 1.10.57 → 1.11.0

package/.claude/commands/monomind/understand.md

@@ -1,139 +0,0 @@
----
-name: monomind:understand
-description: "Monomind — Run semantic enrichment on the current project's monograph knowledge graph. Uses the active Claude Code session for LLM work — no API key needed."
----
-
-# /monomind:understand — Semantic Enrichment
-
-Enriches the current project's monograph knowledge graph with summaries, architectural
-layers, and semantic relationships.
-
-**Designed to run inside Claude Code** — uses YOUR current session for LLM work via
-the Task tool. No `ANTHROPIC_API_KEY` required. The script handles layer detection
-and DB writes; you (Claude) handle per-file summarization.
-
-## Parse Arguments
-
-Parse `$ARGUMENTS` for these flags:
-
-- `--dir <path>`      — project directory (default: cwd)
-- `--db <path>`       — monograph.db path (default: `<dir>/.monomind/monograph.db`)
-- `--full`            — force full re-analysis
-- `--no-llm`          — heuristic-only mode (no per-file summaries)
-- `--layers-only`     — skip per-file analysis, only re-detect layers
-- `--max-files <N>`   — stop after N files (0 = all)
-- `--dry-run`         — show what would happen, don't write
-
-Bare path argument → `--dir`.
-
----
-
-## Step 1: Locate project, DB, and script
-
-```bash
-DIR="${ARGUMENTS_dir:-$(pwd)}"
-DB="${ARGUMENTS_db:-$DIR/.monomind/monograph.db}"
-
-# Find understand-analyze.mjs (ships with monomind globally)
-GLOBAL_ROOT=$(npm root -g 2>/dev/null)
-SCRIPT="$GLOBAL_ROOT/monomind/packages/@monomind/cli/scripts/understand-analyze.mjs"
-[ ! -f "$SCRIPT" ] && SCRIPT="$GLOBAL_ROOT/@monoes/monomindcli/scripts/understand-analyze.mjs"
-```
-
-If `$DB` does not exist:
-> monograph.db not found at `$DB`. Build it first: `npx monomind monograph build`
-
-If `$SCRIPT` does not exist:
-> understand engine missing. Update: `npm install -g monomind@latest`
-
-In either case, STOP.
-
----
-
-## Step 2: Run the script in heuristic mode (always — fast and deterministic)
-
-This step is non-negotiable. The script handles:
-- File node discovery from monograph.db
-- Heuristic layer detection from file paths
-- DB writes (community_id + properties)
-- graph.json emission to `.understand/knowledge-graph.json`
-- Auto-shadowing the DB to `/tmp` when it lives on a network FS
-
-```bash
-node "$SCRIPT" --dir "$DIR" --db "$DB" --no-llm
-```
-
-Wait for completion. Capture stdout. Note how many file nodes were found and how
-many layers were detected. Do NOT advise the user about API keys.
-
----
-
-## Step 3: Per-file summarization (ONLY if `--no-llm` and `--layers-only` are both UNSET)
-
-This is where YOU (the current Claude session) do the LLM work. The script left
-behind a fresh `.understand/knowledge-graph.json` with placeholder summaries.
-
-1. Read `.understand/knowledge-graph.json`. For each node where `properties.fileSummary`
-   is empty or marked `[heuristic]`, do the following:
-   - Use the `Read` tool on `node.file_path` (relative to `$DIR`).
-   - Produce a JSON object: `{ id, fileSummary, tags, complexity, functionSummaries, classSummaries }`
-     where:
-     - `fileSummary`: 1-2 sentences explaining what the file does
-     - `tags`: array of 2-5 short tags
-     - `complexity`: "simple" | "moderate" | "complex"
-     - `functionSummaries`: top-5 functions → 1-sentence each
-     - `classSummaries`: classes → 1-sentence each
-2. Process files in batches of 5 for efficiency. Use `--max-files` to cap if set.
-3. Collect all analyses into an `analyses` array.
-
-If `$ARGUMENTS` includes `--no-llm` or `--layers-only`, SKIP this step entirely.
-
----
-
-## Step 4: Write analyses back to the DB
-
-Pipe the collected analyses to a small re-import:
-
-```bash
-echo "$ANALYSES_JSON" | node "$SCRIPT" --dir "$DIR" --db "$DB" --import-analyses-stdin
-```
-
-(If your `analyses` array is empty, skip this step.)
-
----
-
-## Step 5: Report
-
-```
-╔══════════════════════════════════════════════════╗
-║  /monomind:understand — Enrichment Done           ║
-╠══════════════════════════════════════════════════╣
-║  DB:              .monomind/monograph.db          ║
-║  Files analyzed:  <N>                             ║
-║  LLM summaries:   <N> (via active session)        ║
-║  Layers:          <N>                             ║
-║  graph.json:      .understand/knowledge-graph.json║
-╚══════════════════════════════════════════════════╝
-```
-
-If LLM summaries = 0 (because `--no-llm` was set), say "heuristic-only mode — no per-file summaries written".
-
-Then:
-> Open the Monomind control panel and click **Monograph → GRAPH** to see layers.
-> Each color = one architectural layer (API, Service, Data, UI, etc.).
->
-> Follow-ups:
-> - `/monomind:understand --full` — re-run from scratch
-> - `/monomind:understand --layers-only` — refresh only layers
-> - `/monomind:understand --no-llm` — heuristic-only mode
-
----
-
-## Error Handling
-
-- Do NOT prompt the user to set `ANTHROPIC_API_KEY`. LLM work happens in this session.
-- If the script exits non-zero: show stderr and suggest `npm install -g monomind@latest`.
-- If monograph.db has no file nodes: tell the user to run `npx monomind monograph build` first.
-- All errors are non-fatal — report and return cleanly.
-
-To re-run on a schedule: wrap with `/monomind:repeat`.

package/.claude/commands/training/README.md

@@ -1,39 +0,0 @@
----
-name: training:README
-description: Training skill index — neural pattern training, model optimization, agent specialization, and pattern learning reference
----
-
-# Training Skills
-
-Neural network training, pattern learning, and agent specialization for Monomind.
-
-## Available Skills
-
-- [neural-patterns](./neural-patterns.md) — Overview of how automatic and manual neural training works
-- [neural-train](./neural-train.md) — Train neural patterns with WASM acceleration (MicroLoRA + Flash Attention)
-- [pattern-learn](./pattern-learn.md) — Analyze and store patterns from successful operations
-- [model-update](./model-update.md) — Update and optimize trained neural models
-- [specialization](./specialization.md) — Train agents to specialize in specific domains or file types
-
-## Quick Start
-
-```bash
-# Train coordination patterns (50 epochs, WASM + Flash Attention)
-npx monomind neural train --pattern coordination --epochs 50
-
-# Check neural status
-npx monomind neural status
-
-# Analyze stored patterns
-npx monomind neural patterns --action analyze
-```
-
-## MCP Tools
-
-```javascript
-mcp__monomind__neural_train({ patternType: "coordination", epochs: 50 })
-mcp__monomind__neural_status({})
-mcp__monomind__neural_patterns({ action: "list", limit: 10 })
-mcp__monomind__neural_predict({ input: "task description" })
-mcp__monomind__neural_optimize({ method: "quantize" })
-```

package/.claude/commands/training/neural-patterns.md

@@ -1,73 +0,0 @@
----
-name: training:neural-patterns
-description: Neural pattern training overview — automatic learning from operations, manual training, pattern types, and improvement tracking
----
-
-# Neural Pattern Training
-
-How Monomind continuously learns and improves through neural pattern training.
-
-## How to Invoke
-
-```
-Skill("training:neural-patterns")
-```
-
----
-
-## Automatic Learning
-
-Every successful operation trains the neural networks automatically:
-- Edit patterns for different file types
-- Search strategies that find results faster
-- Task decomposition approaches
-- Agent coordination patterns
-
-The hooks system (`post-edit`, `post-task`) feeds successful operations into training automatically.
-
-## Manual Training
-
-```javascript
-// Train coordination patterns
-mcp__monomind__neural_train({ patternType: "coordination", epochs: 50 })
-
-// Train security patterns with contrastive learning
-mcp__monomind__neural_train({ patternType: "security", epochs: 100 })
-
-// Check training status and pattern scores
-mcp__monomind__neural_status({})
-
-// Analyze recent patterns
-mcp__monomind__neural_patterns({ action: "analyze", limit: 20 })
-```
-
-```bash
-npx monomind neural train --pattern coordination --epochs 50
-npx monomind neural status
-npx monomind neural patterns --action analyze
-```
-
-## Pattern Types
-
-| Pattern | Purpose |
-|---------|---------|
-| `coordination` | Multi-agent task coordination (default) |
-| `optimization` | Performance and resource optimization |
-| `prediction` | Task routing and agent selection |
-| `security` | Security scanning and vulnerability detection |
-| `testing` | Test strategy selection and coverage |
-
-## Improvement Tracking
-
-```javascript
-// View current pattern scores and improvement
-mcp__monomind__neural_status({ verbose: true })
-```
-
-Output includes pattern confidence scores and improvement percentage since last session.
-
-## See Also
-
-- `training:neural-train` — Full training options with WASM acceleration
-- `training:pattern-learn` — Manual pattern storage
-- `training:model-update` — Model optimization

package/.claude/commands/training/neural-train.md

@@ -1,79 +0,0 @@
----
-name: training:neural-train
-description: Train neural patterns with WASM SIMD acceleration — MicroLoRA, Flash Attention (2.49x-7.47x speedup), MoE routing, contrastive learning
----
-
-# Neural Train
-
-Train neural patterns with WASM acceleration using the real `npx monomind neural train` command.
-
-## How to Invoke
-
-```
-Skill("training:neural-train")
-```
-
----
-
-## CLI Reference
-
-```bash
-# Train coordination patterns (default, 50 epochs)
-npx monomind neural train --pattern coordination --epochs 50
-
-# Train with Flash Attention speedup (2.49x-7.47x)
-npx monomind neural train --pattern optimization --flash --epochs 100
-
-# Train security patterns with contrastive learning (InfoNCE)
-npx monomind neural train --pattern security --wasm --contrastive
-
-# Train with Mixture of Experts routing
-npx monomind neural train --pattern coordination --moe --epochs 200
-
-# Train from a data file
-npx monomind neural train --data ./training-data.json --flash
-
-# Curriculum learning (easy → hard)
-npx monomind neural train --pattern prediction --curriculum --epochs 150
-```
-
-## All Flags
-
-| Flag | Default | Description |
-|------|---------|-------------|
-| `--pattern` | `coordination` | Pattern type: coordination, optimization, prediction, security, testing |
-| `--epochs` | `50` | Training epochs |
-| `--data` | — | Training data file path or inline JSON |
-| `--model` | — | Specific model ID to train |
-| `--learning-rate` | `0.01` | Learning rate |
-| `--batch-size` | `32` | Batch size |
-| `--dim` | `256` | Embedding dimension (max 256) |
-| `--wasm` | `true` | Use RuVector WASM SIMD acceleration |
-| `--flash` | `true` | Enable Flash Attention (2.49x-7.47x speedup) |
-| `--moe` | `false` | Enable Mixture of Experts routing (8 experts) |
-| `--hyperbolic` | `false` | Hyperbolic attention for hierarchical patterns |
-| `--contrastive` | `true` | Contrastive learning with InfoNCE loss |
-| `--curriculum` | `false` | Curriculum learning (easy → hard progression) |
-
-## MCP Tools
-
-```javascript
-// Train via MCP
-mcp__monomind__neural_train({ patternType: "coordination", epochs: 50 })
-
-// Check training progress
-mcp__monomind__neural_status({ verbose: true })
-
-// MicroLoRA adaptation
-mcp__monomind__ruvllm_microlora_adapt({ modelId: "coordination", data: trainingData })
-```
-
-## After Training
-
-```bash
-# Verify training improved the model
-npx monomind neural status --verbose
-
-# Export the trained model
-npx monomind neural export --model coordination
-```

package/dist/src/commands/appliance-advanced.d.ts

@@ -1,9 +0,0 @@
-/**
- * CLI Appliance Advanced Commands (Phase 3-4)
- * Sign, publish, and hot-patch RVFA appliances.
- */
-import type { Command } from '../types.js';
-export declare const signCommand: Command;
-export declare const publishCommand: Command;
-export declare const updateAppCommand: Command;
-//# sourceMappingURL=appliance-advanced.d.ts.map

package/dist/src/commands/appliance-advanced.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/commands/appliance-advanced.js

@@ -1,238 +0,0 @@
-/**
- * CLI Appliance Advanced Commands (Phase 3-4)
- * Sign, publish, and hot-patch RVFA appliances.
- */
-import { output } from '../output.js';
-import * as path from 'node:path';
-function fmtSize(bytes) {
-    if (bytes < 1024)
-        return `${bytes} B`;
-    if (bytes < 1024 * 1024)
-        return `${(bytes / 1024).toFixed(1)} KB`;
-    if (bytes < 1024 * 1024 * 1024)
-        return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
-    return `${(bytes / (1024 * 1024 * 1024)).toFixed(2)} GB`;
-}
-function errMsg(err) {
-    return err instanceof Error ? err.message : String(err);
-}
-function checkRelativePath(userPath) {
-    if (!path.isAbsolute(userPath)) {
-        const resolved = path.resolve(userPath);
-        const rel = path.relative(process.cwd(), resolved);
-        if (rel.startsWith('..')) {
-            return `Relative path '${userPath}' escapes the working directory.`;
-        }
-    }
-    return null;
-}
-const fail = (msg, detail) => {
-    output.printError(msg, detail);
-    return { success: false, exitCode: 1 };
-};
-function hdr(title) {
-    output.writeln();
-    output.writeln(output.bold(title));
-    output.writeln(output.dim('─'.repeat(50)));
-    output.writeln();
-}
-async function requireFile(file) {
-    const fs = await import('fs');
-    if (!fs.existsSync(file)) {
-        output.printError(`File not found: ${file}`);
-        return false;
-    }
-    return true;
-}
-// SIGN
-export const signCommand = {
-    name: 'sign',
-    description: 'Sign an RVFA appliance with Ed25519 for tamper detection',
-    options: [
-        { name: 'file', short: 'f', type: 'string', description: 'Path to .rvf file', required: true },
-        { name: 'key', short: 'k', type: 'string', description: 'Path to Ed25519 private key (PEM)' },
-        { name: 'generate-keys', type: 'boolean', description: 'Generate a new key pair' },
-        { name: 'key-dir', type: 'string', description: 'Directory for key storage', default: '.rvfa-keys' },
-        { name: 'signer', type: 'string', description: 'Publisher name for signature metadata' },
-    ],
-    action: async (ctx) => {
-        const file = ctx.flags.file;
-        const keyPath = ctx.flags.key;
-        const genKeys = ctx.flags['generate-keys'];
-        const keyDir = ctx.flags['key-dir'] || '.rvfa-keys';
-        const signer = ctx.flags.signer;
-        if (!file)
-            return fail('--file is required');
-        try {
-            const signing = await import('../appliance/rvfa-signing.js');
-            if (genKeys) {
-                hdr('Generating Ed25519 Key Pair');
-                const kp = await signing.generateKeyPair();
-                const paths = await signing.saveKeyPair(kp, keyDir);
-                output.printSuccess(`Public key:  ${paths.publicKeyPath}`);
-                output.printSuccess(`Private key: ${paths.privateKeyPath}`);
-                output.printInfo(`Fingerprint: ${kp.fingerprint}`);
-                output.writeln(output.dim('  Keep the private key secure. Share only the public key.'));
-                output.writeln();
-            }
-            if (!(await requireFile(file)))
-                return { success: false, exitCode: 1 };
-            hdr('Signing RVFA Appliance');
-            let privateKey;
-            if (keyPath) {
-                const pathErr = checkRelativePath(keyPath);
-                if (pathErr)
-                    return fail(pathErr);
-                const fs = await import('fs');
-                privateKey = fs.readFileSync(keyPath);
-            }
-            else {
-                const kp = await signing.loadKeyPair(keyDir);
-                privateKey = kp.privateKey;
-            }
-            const s = new signing.RvfaSigner(privateKey);
-            const meta = await s.signAppliance(file, signer);
-            output.printSuccess('Appliance signed successfully');
-            output.printInfo(`Algorithm:   ${meta.algorithm}`);
-            output.printInfo(`Fingerprint: ${meta.publicKeyFingerprint}`);
-            output.printInfo(`Signed at:   ${meta.signedAt}`);
-            if (signer)
-                output.printInfo(`Signed by:   ${signer}`);
-            output.printInfo(`Signature:   ${meta.signature.slice(0, 32)}...`);
-            return { success: true, data: meta };
-        }
-        catch (err) {
-            return fail('Signing failed', errMsg(err));
-        }
-    },
-};
-// PUBLISH
-export const publishCommand = {
-    name: 'publish',
-    description: 'Publish an RVFA appliance to IPFS via Pinata',
-    options: [
-        { name: 'file', short: 'f', type: 'string', description: 'Path to .rvf file', required: true },
-        { name: 'name', short: 'n', type: 'string', description: 'Publication name' },
-        { name: 'description', type: 'string', description: 'Description' },
-    ],
-    action: async (ctx) => {
-        const file = ctx.flags.file;
-        if (!file)
-            return fail('--file is required');
-        if (!(await requireFile(file)))
-            return { success: false, exitCode: 1 };
-        try {
-            const dist = await import('../appliance/rvfa-distribution.js');
-            hdr('Publishing RVFA to IPFS');
-            output.printInfo(`File: ${file}`);
-            output.writeln();
-            const publisher = dist.createPublisher();
-            const result = await publisher.publish(file, {
-                name: ctx.flags.name,
-                description: ctx.flags.description,
-            });
-            output.printSuccess('Published successfully');
-            output.printInfo(`CID:     ${output.bold(result.cid)}`);
-            output.printInfo(`Size:    ${fmtSize(result.size)}`);
-            output.printInfo(`Gateway: ${result.gatewayUrl}`);
-            return { success: true, data: result };
-        }
-        catch (err) {
-            return fail('Publishing failed', errMsg(err));
-        }
-    },
-};
-// UPDATE (hot-patch)
-export const updateAppCommand = {
-    name: 'update',
-    description: 'Hot-patch a section in an RVFA appliance',
-    options: [
-        { name: 'file', short: 'f', type: 'string', description: 'Path to .rvf file', required: true },
-        { name: 'section', short: 's', type: 'string', description: 'Section to patch (e.g. monomind, models)', required: true },
-        { name: 'patch', short: 'p', type: 'string', description: 'Path to .rvfp patch file' },
-        { name: 'data', short: 'd', type: 'string', description: 'Path to new section data (creates patch automatically)' },
-        { name: 'version', type: 'string', description: 'Patch version', default: '0.0.1' },
-        { name: 'no-backup', type: 'boolean', description: 'Skip backup creation' },
-        { name: 'public-key', type: 'string', description: 'Path to public key for patch verification' },
-    ],
-    action: async (ctx) => {
-        const file = ctx.flags.file;
-        const section = ctx.flags.section;
-        const patchPath = ctx.flags.patch;
-        const dataPath = ctx.flags.data;
-        if (!file || !section)
-            return fail('--file and --section are required');
-        if (!patchPath && !dataPath)
-            return fail('Provide --patch (RVFP file) or --data (raw section data)');
-        if (!(await requireFile(file)))
-            return { success: false, exitCode: 1 };
-        try {
-            const dist = await import('../appliance/rvfa-distribution.js');
-            const { RvfaReader } = await import('../appliance/rvfa-format.js');
-            const fs = await import('fs');
-            hdr('RVFA Hot-Patch Update');
-            output.printInfo(`Appliance: ${file}`);
-            output.printInfo(`Section:   ${section}`);
-            output.writeln();
-            let patchBuf;
-            if (patchPath) {
-                const patchPathErr = checkRelativePath(patchPath);
-                if (patchPathErr)
-                    return fail(patchPathErr);
-                if (!(await requireFile(patchPath)))
-                    return { success: false, exitCode: 1 };
-                patchBuf = fs.readFileSync(patchPath);
-                output.printInfo(`Patch file: ${patchPath} (${fmtSize(patchBuf.length)})`);
-            }
-            else {
-                const dataPathErr = checkRelativePath(dataPath);
-                if (dataPathErr)
-                    return fail(dataPathErr);
-                if (!(await requireFile(dataPath)))
-                    return { success: false, exitCode: 1 };
-                const newData = fs.readFileSync(dataPath);
-                const reader = await RvfaReader.fromFile(file);
-                const appHdr = reader.getHeader();
-                output.printInfo(`Creating patch for section "${section}" (${fmtSize(newData.length)} new data)`);
-                patchBuf = await dist.RvfaPatcher.createPatch({
-                    targetName: appHdr.name,
-                    targetVersion: appHdr.appVersion,
-                    sectionId: section,
-                    sectionData: newData,
-                    patchVersion: ctx.flags.version || '0.0.1',
-                    compression: 'gzip',
-                });
-            }
-            let pubKey;
-            if (ctx.flags['public-key']) {
-                const pkPath = ctx.flags['public-key'];
-                const pkPathErr = checkRelativePath(pkPath);
-                if (pkPathErr)
-                    return fail(pkPathErr);
-                if (!(await requireFile(pkPath)))
-                    return { success: false, exitCode: 1 };
-                pubKey = fs.readFileSync(pkPath);
-            }
-            const result = await dist.RvfaPatcher.applyPatch(file, patchBuf, {
-                backup: !ctx.flags['no-backup'],
-                verify: true,
-                publicKey: pubKey,
-            });
-            if (result.success) {
-                output.printSuccess(`Section "${result.patchedSection}" updated successfully`);
-                output.printInfo(`New size: ${fmtSize(result.newSize)}`);
-                if (result.backupPath)
-                    output.printInfo(`Backup:  ${result.backupPath}`);
-            }
-            else {
-                output.printError('Patch failed');
-                result.errors.forEach(e => output.writeln(`  ${output.error('X')} ${e}`));
-            }
-            return { success: result.success, exitCode: result.success ? 0 : 1, data: result };
-        }
-        catch (err) {
-            return fail('Update failed', errMsg(err));
-        }
-    },
-};
-//# sourceMappingURL=appliance-advanced.js.map

package/dist/src/commands/appliance-advanced.js.map

@@ -1 +0,0 @@
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package/dist/src/commands/appliance.d.ts

@@ -1,8 +0,0 @@
-/**
- * CLI Appliance Command
- * Self-contained RVFA appliance management (build, inspect, verify, extract, run, sign, publish, update)
- */
-import type { Command } from '../types.js';
-export declare const applianceCommand: Command;
-export default applianceCommand;
-//# sourceMappingURL=appliance.d.ts.map

package/dist/src/commands/appliance.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"appliance.d.ts","sourceRoot":"","sources":["../../../src/commands/appliance.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAiC,MAAM,aAAa,CAAC;AA4Y1E,eAAO,MAAM,gBAAgB,EAAE,OA0C9B,CAAC;AAEF,eAAe,gBAAgB,CAAC"}