causantic 0.7.2 → 0.8.0

package/README.md

@@ -72,8 +72,8 @@ All data stays on your machine. Optional per-chunk encryption (ChaCha20-Poly1305
 **2. Hybrid BM25 + Vector Search**
 Vector search finds chunks that _look similar_. BM25 keyword search finds chunks with _exact lexical matches_ — function names, error codes, CLI flags. Both run in parallel and fuse via Reciprocal Rank Fusion (RRF).
 
-**3. Sequential Causal Graph with Episodic Chain Walking**
-Chunks are connected in a sequential linked list — intra-turn chunks chained sequentially, inter-turn edges linking last→first, cross-session edges bridging sessions. The `recall` tool walks this graph backward to reconstruct episodic narratives; `predict` walks forward. Chains are scored by cosine similarity per token, producing ordered narratives where each chunk adds new information.
+**3. Causal Graph with Multi-Path Chain Walking**
+Chunks are connected in a sequential linked list — intra-turn chunks chained sequentially, inter-turn edges linking last→first, cross-session edges bridging sessions. The `recall` tool walks this graph backward to reconstruct episodic narratives; `predict` walks forward. At branching points (agent transitions, cross-session links), multi-path DFS explores all alternatives and selects the best chain by median cosine similarity, producing ordered narratives where each chunk adds new information.
 
 **4. HDBSCAN Cluster-Guided Expansion**
 Topic clusters group semantically related chunks. During retrieval, results expand through cluster siblings — surfacing context that neither vector nor keyword search found independently. Native TypeScript implementation (130× faster than hdbscan-ts).
@@ -189,7 +189,7 @@ Or run `npx causantic init` to configure automatically.
 
 ## Skills
 
-Causantic installs 14 Claude Code slash commands (via `npx causantic init`) for natural-language interaction with memory:
+Causantic installs 15 Claude Code slash commands (via `npx causantic init`) for natural-language interaction with memory:
 
 | Skill                           | Description                                                                                                          |
 | ------------------------------- | -------------------------------------------------------------------------------------------------------------------- |
@@ -206,6 +206,7 @@ Causantic installs 14 Claude Code slash commands (via `npx causantic init`) for
 | `/causantic-crossref [pattern]` | Search across all projects for reusable patterns                                                                     |
 | `/causantic-retro [scope]`      | Surface recurring patterns, problems, and decisions across sessions                                                  |
 | `/causantic-cleanup`            | Memory-informed codebase review and cleanup plan                                                                     |
+| `/causantic-roadmap [goal]`     | Gather deferred work and goals into a phased roadmap                                                                 |
 | `/causantic-forget [query]`     | Delete memory by topic, time range, or session (always previews first)                                               |
 
 Skills are installed to `~/.claude/skills/causantic-*/` and work as slash commands in Claude Code. They orchestrate the MCP tools above with structured prompts tailored to each use case.
@@ -274,7 +275,7 @@ See [Security Guide](docs/guides/security.md).
 - [User Guides](docs/guides/) — Dashboard, benchmarking, integration, security, maintenance
 - [CLI Reference](docs/reference/cli-commands.md) — All commands and options
 - [MCP Tools Reference](docs/reference/mcp-tools.md) — Tool schemas and usage
-- [Skills Reference](docs/reference/skills.md) — All 14 slash commands
+- [Skills Reference](docs/reference/skills.md) — All 15 slash commands
 - [Configuration Reference](docs/reference/configuration.md) — All configuration options
 - [Research Documentation](docs/research/) — Experiment results and design decisions
 - [Design Decision Log](docs/research/decisions.md) — Why things are the way they are

package/config.schema.json

@@ -22,6 +22,13 @@
           "maximum": 100,
           "default": 4,
           "description": "Minimum points required to form a cluster"
+        },
+        "incrementalThreshold": {
+          "type": "number",
+          "minimum": 0.01,
+          "maximum": 1,
+          "default": 0.3,
+          "description": "Ratio of new chunks (vs total at last full recluster) that triggers a full recluster. 0.3 = 30%."
         }
       },
       "additionalProperties": false
@@ -93,6 +100,11 @@
           "maximum": 1000,
           "default": 30,
           "description": "Rate limit for LLM refresh calls per minute"
+        },
+        "enableLabelling": {
+          "type": "boolean",
+          "default": true,
+          "description": "Enable LLM-based cluster labelling. Requires Anthropic API key. Set to false for fully local usage without an API key."
         }
       },
       "additionalProperties": false
@@ -156,6 +168,12 @@
           "enum": ["auto", "coreml", "cuda", "cpu", "wasm"],
           "default": "auto",
           "description": "Device for embedding inference. 'auto' detects hardware capabilities."
+        },
+        "model": {
+          "type": "string",
+          "enum": ["jina-small", "nomic-v1.5", "jina-code", "bge-small"],
+          "default": "jina-small",
+          "description": "Embedding model. Changing model requires running 'npx causantic reindex' to re-embed all chunks."
         }
       },
       "additionalProperties": false
@@ -184,6 +202,34 @@
           "maximum": 1,
           "default": 0.7,
           "description": "MMR lambda: 0 = pure diversity, 1 = pure relevance"
+        },
+        "feedbackWeight": {
+          "type": "number",
+          "minimum": 0,
+          "maximum": 1,
+          "default": 0.1,
+          "description": "How much retrieval feedback influences cluster expansion scoring. 0 = disabled, 1 = maximum influence."
+        }
+      },
+      "additionalProperties": false
+    },
+    "recency": {
+      "type": "object",
+      "description": "Recency boost settings for time-decay scoring",
+      "properties": {
+        "decayFactor": {
+          "type": "number",
+          "minimum": 0,
+          "maximum": 1,
+          "default": 0.3,
+          "description": "Amplitude of the time-decay boost (multiplied by exp decay)"
+        },
+        "halfLifeHours": {
+          "type": "number",
+          "minimum": 1,
+          "maximum": 8760,
+          "default": 48,
+          "description": "Half-life in hours for the decay function"
         }
       },
       "additionalProperties": false

package/dist/cli/commands/init/api-key.d.ts

@@ -0,0 +1,2 @@
+export declare function offerApiKeySetup(): Promise<void>;
+//# sourceMappingURL=api-key.d.ts.map

package/dist/cli/commands/init/api-key.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"api-key.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/init/api-key.ts"],"names":[],"mappings":"AAGA,wBAAsB,gBAAgB,IAAI,OAAO,CAAC,IAAI,CAAC,CAuBtD"}

package/dist/cli/commands/init/api-key.js

@@ -0,0 +1,26 @@
+import { createSecretStore } from '../../../utils/secret-store.js';
+import { promptPassword, promptYesNo } from '../../utils.js';
+export async function offerApiKeySetup() {
+    console.log('');
+    console.log('Cluster labeling uses Claude Haiku to generate human-readable');
+    console.log('descriptions for topic clusters.');
+    if (!(await promptYesNo('Add Anthropic API key for cluster labeling?')))
+        return;
+    const apiKey = await promptPassword('Enter Anthropic API key: ');
+    if (apiKey && apiKey.startsWith('sk-ant-')) {
+        const store = createSecretStore();
+        await store.set('anthropic-api-key', apiKey);
+        console.log('\u2713 API key stored in system keychain');
+        // Set in env so update-clusters can use it for labeling
+        process.env.ANTHROPIC_API_KEY = apiKey;
+    }
+    else if (apiKey) {
+        console.log('\u26a0 Invalid API key format (should start with sk-ant-)');
+        console.log('  You can add it later with: causantic config set-key anthropic-api-key');
+    }
+    else {
+        console.log('  Skipping — clusters will be unlabeled.');
+        console.log('  Add a key later with: causantic config set-key anthropic-api-key');
+    }
+}
+//# sourceMappingURL=api-key.js.map

package/dist/cli/commands/init/api-key.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/encryption.d.ts

@@ -0,0 +1,2 @@
+export declare function setupEncryption(causanticDir: string): Promise<boolean>;
+//# sourceMappingURL=encryption.d.ts.map

package/dist/cli/commands/init/encryption.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/encryption.js

@@ -0,0 +1,104 @@
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { getDb, storeDbKey } from '../../../storage/db.js';
+import { promptYesNo } from '../../utils.js';
+export async function setupEncryption(causanticDir) {
+    const dbPath = path.join(causanticDir, 'memory.db');
+    const existingDbExists = fs.existsSync(dbPath) && fs.statSync(dbPath).size > 0;
+    let existingDbIsUnencrypted = false;
+    if (existingDbExists) {
+        try {
+            const Database = (await import('better-sqlite3-multiple-ciphers')).default;
+            const testDb = new Database(dbPath);
+            testDb.prepare('SELECT 1').get();
+            testDb.close();
+            existingDbIsUnencrypted = true;
+        }
+        catch {
+            // DB exists but can't be opened without key — may already be encrypted
+        }
+    }
+    console.log('');
+    console.log('Enable database encryption?');
+    console.log('Protects conversation data, embeddings, and work patterns.');
+    if (existingDbIsUnencrypted) {
+        console.log('');
+        console.log('\u26a0  Existing unencrypted database detected.');
+        console.log('  Enabling encryption will back up the existing database and create a new encrypted one.');
+        console.log('  Your data will be migrated automatically.');
+    }
+    if (!(await promptYesNo('Enable encryption?')))
+        return false;
+    const { generatePassword } = await import('../../../storage/encryption.js');
+    if (existingDbIsUnencrypted) {
+        const backupPath = dbPath + '.unencrypted.bak';
+        fs.copyFileSync(dbPath, backupPath);
+        console.log(`\u2713 Backed up existing database to ${path.basename(backupPath)}`);
+        fs.unlinkSync(dbPath);
+        for (const suffix of ['-wal', '-shm']) {
+            const walPath = dbPath + suffix;
+            if (fs.existsSync(walPath))
+                fs.unlinkSync(walPath);
+        }
+    }
+    console.log('');
+    console.log('Generating encryption key...');
+    const key = generatePassword(32);
+    await storeDbKey(key);
+    const configPath = path.join(causanticDir, 'config.json');
+    const existingConfig = fs.existsSync(configPath)
+        ? JSON.parse(fs.readFileSync(configPath, 'utf-8'))
+        : {};
+    fs.writeFileSync(configPath, JSON.stringify({
+        ...existingConfig,
+        encryption: { enabled: true, cipher: 'chacha20', keySource: 'keychain' },
+    }, null, 2));
+    console.log('\u2713 Key stored in system keychain');
+    console.log('\u2713 Encryption enabled with ChaCha20-Poly1305');
+    if (existingDbIsUnencrypted) {
+        await migrateToEncryptedDb(dbPath);
+    }
+    return true;
+}
+async function migrateToEncryptedDb(dbPath) {
+    const backupPath = dbPath + '.unencrypted.bak';
+    try {
+        const newDb = getDb();
+        const Database = (await import('better-sqlite3-multiple-ciphers')).default;
+        const oldDb = new Database(backupPath);
+        // Skip schema_version (handled by migrations) and FTS5 shadow tables
+        // (populated automatically via triggers when chunks are inserted)
+        const tables = oldDb
+            .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name != 'schema_version' AND name NOT LIKE 'chunks_fts%'")
+            .all();
+        let migratedRows = 0;
+        for (const { name } of tables) {
+            const exists = newDb
+                .prepare("SELECT 1 FROM sqlite_master WHERE type='table' AND name=?")
+                .get(name);
+            if (!exists)
+                continue;
+            const rows = oldDb.prepare(`SELECT * FROM "${name}"`).all();
+            if (rows.length === 0)
+                continue;
+            const columns = Object.keys(rows[0]);
+            const placeholders = columns.map(() => '?').join(', ');
+            const insert = newDb.prepare(`INSERT OR IGNORE INTO "${name}" (${columns.map((c) => `"${c}"`).join(', ')}) VALUES (${placeholders})`);
+            const batchInsert = newDb.transaction((rowBatch) => {
+                for (const row of rowBatch) {
+                    insert.run(...columns.map((c) => row[c]));
+                }
+            });
+            batchInsert(rows);
+            migratedRows += rows.length;
+        }
+        oldDb.close();
+        console.log(`\u2713 Migrated ${migratedRows} rows to encrypted database`);
+    }
+    catch (err) {
+        console.log(`\u26a0 Migration error: ${err.message}`);
+        console.log(`  Backup preserved at: ${backupPath}`);
+        console.log('  You can manually re-import with: causantic import');
+    }
+}
+//# sourceMappingURL=encryption.js.map

package/dist/cli/commands/init/encryption.js.map

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package/dist/cli/commands/init/health.d.ts

@@ -0,0 +1,2 @@
+export declare function runHealthCheck(): Promise<void>;
+//# sourceMappingURL=health.d.ts.map

package/dist/cli/commands/init/health.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/health.js

@@ -0,0 +1,15 @@
+export async function runHealthCheck() {
+    console.log('');
+    console.log('Running health check...');
+    try {
+        const { vectorStore } = await import('../../../storage/vector-store.js');
+        if (vectorStore && typeof vectorStore.count === 'function') {
+            await vectorStore.count();
+        }
+        console.log('\u2713 Vector store OK');
+    }
+    catch (error) {
+        console.log(`\u26a0 Vector store: ${error.message}`);
+    }
+}
+//# sourceMappingURL=health.js.map

package/dist/cli/commands/init/health.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/hooks.d.ts

@@ -0,0 +1,2 @@
+export declare function configureHooks(claudeConfigPath: string): Promise<void>;
+//# sourceMappingURL=hooks.d.ts.map

package/dist/cli/commands/init/hooks.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/hooks.js

@@ -0,0 +1,92 @@
+import * as fs from 'node:fs';
+import { getCliEntryPath } from './shared.js';
+export async function configureHooks(claudeConfigPath) {
+    try {
+        const settingsContent = fs.readFileSync(claudeConfigPath, 'utf-8');
+        const config = JSON.parse(settingsContent);
+        const cliEntry = getCliEntryPath();
+        const nodeBin = process.execPath;
+        const causanticHooks = [
+            {
+                event: 'PreCompact',
+                matcher: '',
+                hook: {
+                    type: 'command',
+                    command: `${nodeBin} ${cliEntry} hook pre-compact`,
+                    timeout: 300,
+                    async: true,
+                },
+            },
+            {
+                event: 'SessionStart',
+                matcher: '',
+                hook: {
+                    type: 'command',
+                    command: `${nodeBin} ${cliEntry} hook session-start`,
+                    timeout: 60,
+                },
+            },
+            {
+                event: 'SessionEnd',
+                matcher: '',
+                hook: {
+                    type: 'command',
+                    command: `${nodeBin} ${cliEntry} hook session-end`,
+                    timeout: 300,
+                    async: true,
+                },
+            },
+            {
+                event: 'SessionEnd',
+                matcher: '',
+                hook: {
+                    type: 'command',
+                    command: `${nodeBin} ${cliEntry} hook claudemd-generator`,
+                    timeout: 60,
+                    async: true,
+                },
+            },
+        ];
+        if (!config.hooks) {
+            config.hooks = {};
+        }
+        // Extract the hook subcommand (e.g. "hook pre-compact") used to detect
+        // existing entries regardless of the install path that preceded it.
+        const hookSubcommand = (cmd) => {
+            const match = cmd.match(/hook\s+\S+/);
+            return match ? match[0] : cmd;
+        };
+        let hooksChanged = 0;
+        for (const { event, matcher, hook } of causanticHooks) {
+            if (!config.hooks[event]) {
+                config.hooks[event] = [];
+            }
+            const subCmd = hookSubcommand(hook.command);
+            // Check if an identical entry already exists (same hook object).
+            const hookStr = JSON.stringify(hook);
+            const exactMatch = config.hooks[event].some((entry) => entry.hooks?.some((h) => JSON.stringify(h) === hookStr));
+            if (exactMatch)
+                continue;
+            // Remove any stale entries for the same hook subcommand (e.g. from a
+            // different install path) so we don't accumulate duplicates.
+            config.hooks[event] = config.hooks[event].filter((entry) => !entry.hooks?.some((h) => h.command && hookSubcommand(h.command) === subCmd));
+            config.hooks[event].push({
+                matcher,
+                hooks: [hook],
+            });
+            hooksChanged++;
+        }
+        if (hooksChanged > 0) {
+            fs.writeFileSync(claudeConfigPath, JSON.stringify(config, null, 2));
+            const hookNames = causanticHooks.map((h) => h.event).join(', ');
+            console.log(`\u2713 Configured ${hooksChanged} Claude Code hooks (${hookNames})`);
+        }
+        else {
+            console.log('\u2713 Claude Code hooks already configured');
+        }
+    }
+    catch {
+        console.log('\u26a0 Could not configure Claude Code hooks');
+    }
+}
+//# sourceMappingURL=hooks.js.map

package/dist/cli/commands/init/hooks.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/index.d.ts

@@ -0,0 +1,3 @@
+import type { Command } from '../../types.js';
+export declare const initCommand: Command;
+//# sourceMappingURL=index.d.ts.map

package/dist/cli/commands/init/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init/index.js

@@ -0,0 +1,95 @@
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import * as os from 'node:os';
+import { getDb } from '../../../storage/db.js';
+import { setupEncryption } from './encryption.js';
+import { migrateMcpFromSettings, configureMcp, patchProjectMcpFiles } from './mcp-config.js';
+import { configureHooks } from './hooks.js';
+import { installSkillsAndClaudeMd } from './skills.js';
+import { runHealthCheck } from './health.js';
+import { offerBatchIngest } from './ingest.js';
+function checkNodeVersion() {
+    const nodeVersion = process.versions.node;
+    const majorVersion = parseInt(nodeVersion.split('.')[0], 10);
+    if (majorVersion >= 20) {
+        console.log(`\u2713 Node.js ${nodeVersion}`);
+    }
+    else {
+        console.log(`\u2717 Node.js ${nodeVersion} (requires 20+)`);
+        process.exit(1);
+    }
+}
+function createDirectoryStructure(causanticDir) {
+    const vectorsDir = path.join(causanticDir, 'vectors');
+    for (const dir of [causanticDir, vectorsDir]) {
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+            console.log(`\u2713 Created ${dir}`);
+        }
+        else {
+            console.log(`\u2713 Directory exists: ${dir}`);
+        }
+    }
+}
+function initializeDatabase(encryptionEnabled) {
+    try {
+        const db = getDb();
+        db.prepare('SELECT 1').get();
+        console.log('\u2713 Database initialized' + (encryptionEnabled ? ' (encrypted)' : ''));
+    }
+    catch (error) {
+        console.log(`\u2717 Database error: ${error.message}`);
+        process.exit(1);
+    }
+}
+export const initCommand = {
+    name: 'init',
+    description: 'Initialize Causantic (setup wizard)',
+    usage: 'causantic init [--skip-mcp] [--skip-encryption] [--skip-ingest]',
+    handler: async (args) => {
+        const skipMcp = args.includes('--skip-mcp');
+        const skipEncryption = args.includes('--skip-encryption');
+        const skipIngest = args.includes('--skip-ingest');
+        console.log('Causantic - Setup');
+        console.log('=================');
+        console.log('');
+        checkNodeVersion();
+        const causanticDir = path.join(os.homedir(), '.causantic');
+        createDirectoryStructure(causanticDir);
+        let encryptionEnabled = false;
+        if (!skipEncryption && process.stdin.isTTY) {
+            encryptionEnabled = await setupEncryption(causanticDir);
+        }
+        initializeDatabase(encryptionEnabled);
+        const claudeConfigPath = path.join(os.homedir(), '.claude', 'settings.json');
+        const mcpConfigPath = path.join(os.homedir(), '.claude.json');
+        console.log('');
+        if (!skipMcp) {
+            migrateMcpFromSettings(claudeConfigPath, mcpConfigPath);
+            await configureMcp(mcpConfigPath);
+            if (process.stdin.isTTY) {
+                await patchProjectMcpFiles();
+            }
+            await installSkillsAndClaudeMd();
+            await configureHooks(claudeConfigPath);
+        }
+        await runHealthCheck();
+        if (!skipIngest && process.stdin.isTTY) {
+            await offerBatchIngest();
+        }
+        console.log('');
+        console.log('Setup complete!');
+        console.log('');
+        console.log('Next steps:');
+        if (!skipIngest && process.stdin.isTTY) {
+            console.log('  1. Restart Claude Code');
+            console.log('  2. Ask Claude: "What did we work on recently?"');
+        }
+        else {
+            console.log('  1. npx causantic batch-ingest ~/.claude/projects');
+            console.log('  2. Restart Claude Code');
+            console.log('  3. Ask Claude: "What did we work on recently?"');
+        }
+    },
+};
+//# sourceMappingURL=index.js.map

package/dist/cli/commands/init/index.js.map

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package/dist/cli/commands/init/ingest.d.ts

@@ -0,0 +1,2 @@
+export declare function offerBatchIngest(): Promise<void>;
+//# sourceMappingURL=ingest.d.ts.map

package/dist/cli/commands/init/ingest.d.ts.map

@@ -0,0 +1 @@
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