gnosys 5.0.1 → 5.1.0

package/dist/cli.js

@@ -27,7 +27,7 @@ import { GnosysAsk } from "./lib/ask.js";
 import { getLLMProvider, isProviderAvailable } from "./lib/llm.js";
 import { GnosysDB } from "./lib/db.js";
 import { migrate, formatMigrationReport } from "./lib/migrate.js";
-import { createProjectIdentity, readProjectIdentity, findProjectIdentity } from "./lib/projectIdentity.js";
+import { createProjectIdentity, readProjectIdentity, findProjectIdentity, migrateProject } from "./lib/projectIdentity.js";
 import { setPreference, getPreference, getAllPreferences, deletePreference } from "./lib/preferences.js";
 import { syncToTarget } from "./lib/rulesGen.js";
 // Load API keys from ~/.config/gnosys/.env (same as MCP server)
@@ -389,29 +389,51 @@ program
     }
     console.log("Structuring memory via LLM...");
     const result = await ingestion.ingest(input);
-    const id = await writeTarget.store.generateId(result.category);
-    const today = new Date().toISOString().split("T")[0];
-    const frontmatter = {
-        id,
-        title: result.title,
-        category: result.category,
-        tags: result.tags,
-        relevance: result.relevance,
-        author: opts.author,
-        authority: opts.authority,
-        confidence: result.confidence,
-        created: today,
-        modified: today,
-        last_reviewed: today,
-        status: "active",
-        supersedes: null,
-    };
-    const content = `# ${result.title}\n\n${result.content}`;
-    const relPath = await writeTarget.store.writeMemory(result.category, `${result.filename}.md`, frontmatter, content);
-    console.log(`\nMemory added to [${writeTarget.label}]: ${result.title}`);
-    console.log(`Path: ${writeTarget.label}:${relPath}`);
-    console.log(`Category: ${result.category}`);
-    console.log(`Confidence: ${result.confidence}`);
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        const projectId = await resolveProjectId();
+        const id = centralDb.getNextId(result.category, projectId || undefined);
+        const today = new Date().toISOString().split("T")[0];
+        const now = new Date().toISOString();
+        const content = `# ${result.title}\n\n${result.content}`;
+        const tags = result.tags;
+        const tagsJson = Array.isArray(tags)
+            ? JSON.stringify(tags)
+            : JSON.stringify(Object.values(tags).flat());
+        centralDb.insertMemory({
+            id,
+            title: result.title,
+            category: result.category,
+            content,
+            summary: null,
+            tags: tagsJson,
+            relevance: result.relevance,
+            author: opts.author,
+            authority: opts.authority,
+            confidence: result.confidence,
+            reinforcement_count: 0,
+            content_hash: "",
+            status: "active",
+            tier: "active",
+            supersedes: null,
+            superseded_by: null,
+            last_reinforced: null,
+            created: now,
+            modified: now,
+            embedding: null,
+            source_path: null,
+            project_id: projectId,
+            scope: "project",
+        });
+        console.log(`\nMemory added to [${writeTarget.label}]: ${result.title}`);
+        console.log(`ID: ${id}`);
+        console.log(`Category: ${result.category}`);
+        console.log(`Confidence: ${result.confidence}`);
+    }
+    finally {
+        centralDb?.close();
+    }
     if (result.proposedNewTags && result.proposedNewTags.length > 0) {
         console.log("\nProposed new tags (not yet in registry):");
         for (const t of result.proposedNewTags) {
@@ -452,6 +474,7 @@ program
         // Good — fresh init
     }
     if (!isResync) {
+        // Create directory structure (DB is sole source of truth — no category folders or changelog)
         await fs.mkdir(storePath, { recursive: true });
         await fs.mkdir(path.join(storePath, ".config"), { recursive: true });
         const defaultRegistry = {
@@ -475,27 +498,6 @@ program
         // Create .gitignore inside .gnosys to exclude large binary attachments
         const storeGitignore = "# Large binary attachments (tracked via manifest, not git)\nattachments/\n";
         await fs.writeFile(path.join(storePath, ".gitignore"), storeGitignore, "utf-8");
-        const changelog = `# Gnosys Changelog\n\n## ${new Date().toISOString().split("T")[0]}\n\n- Store initialized\n`;
-        await fs.writeFile(path.join(storePath, "CHANGELOG.md"), changelog, "utf-8");
-        try {
-            const { execSync } = await import("child_process");
-            execSync("git init", { cwd: storePath, stdio: "pipe" });
-            try {
-                execSync("git config user.name", { cwd: storePath, stdio: "pipe" });
-            }
-            catch {
-                execSync('git config user.name "Gnosys"', { cwd: storePath, stdio: "pipe" });
-                execSync('git config user.email "gnosys@local"', { cwd: storePath, stdio: "pipe" });
-            }
-            execSync("git add -A && git add -f .config/", { cwd: storePath, stdio: "pipe" });
-            execSync('git commit -m "Initialize Gnosys store"', {
-                cwd: storePath,
-                stdio: "pipe",
-            });
-        }
-        catch {
-            // Git not available
-        }
     }
     // v3.0: Create/update project identity and register in central DB
     let centralDb = null;
@@ -547,11 +549,183 @@ program
         console.log(`  gnosys.json   (project identity)`);
         console.log(`  .config/      (internal config)`);
         console.log(`  tags.json     (tag registry)`);
-        console.log(`  CHANGELOG.md`);
-        console.log(`  git repo`);
     }
     console.log(`\nStart adding memories with: gnosys add "your knowledge here"`);
 });
+// ─── gnosys migrate ─────────────────────────────────────────────────────
+program
+    .command("migrate")
+    .description("Interactively migrate a .gnosys/ store to a new directory. Moves files, updates project name/paths, syncs to central DB, and cleans up.")
+    .option("--from <dir>", "Source directory containing .gnosys/ (skips prompt)")
+    .option("--to <dir>", "Target directory to move .gnosys/ into (skips prompt)")
+    .option("--name <name>", "New project name (skips prompt, default: basename of target)")
+    .option("--yes", "Skip all confirmation prompts (non-interactive mode)")
+    .action(async (opts) => {
+    const { createInterface } = await import("readline/promises");
+    const rl = opts.yes ? null : createInterface({ input: process.stdin, output: process.stdout });
+    const ask = async (question, defaultValue) => {
+        if (!rl)
+            return defaultValue || "";
+        const suffix = defaultValue ? ` (${defaultValue})` : "";
+        const answer = (await rl.question(`${question}${suffix}: `)).trim();
+        return answer || defaultValue || "";
+    };
+    try {
+        console.log("\n── Gnosys Project Migration ──\n");
+        // 1. Resolve source
+        let sourceDir;
+        if (opts.from) {
+            sourceDir = path.resolve(opts.from);
+        }
+        else {
+            // Try auto-detect first
+            const found = await findProjectIdentity(process.cwd());
+            const defaultSource = found ? found.projectRoot : "";
+            const sourceInput = await ask("Source directory (contains .gnosys/)", defaultSource);
+            if (!sourceInput) {
+                console.error("No source directory provided.");
+                rl?.close();
+                process.exit(1);
+            }
+            sourceDir = path.resolve(sourceInput);
+        }
+        // Verify source has .gnosys/
+        const storePath = path.join(sourceDir, ".gnosys");
+        try {
+            await fs.stat(storePath);
+        }
+        catch {
+            console.error(`No .gnosys/ directory found at ${sourceDir}`);
+            rl?.close();
+            process.exit(1);
+        }
+        // Read identity (may not exist for pre-v3 stores)
+        const identity = await readProjectIdentity(sourceDir);
+        // Count memory files
+        const { glob } = await import("glob");
+        const memFiles = await glob("**/*.md", {
+            cwd: storePath,
+            ignore: ["**/CHANGELOG.md", "**/MANIFEST.md", "**/.git/**", "**/.obsidian/**"],
+        });
+        console.log("\nSource project:");
+        if (identity) {
+            console.log(`  Name:      ${identity.projectName}`);
+            console.log(`  ID:        ${identity.projectId}`);
+        }
+        else {
+            console.log(`  Name:      (unregistered — pre-v3 store)`);
+        }
+        console.log(`  Directory: ${sourceDir}`);
+        console.log(`  Memories:  ${memFiles.length} markdown files`);
+        // 2. Resolve target
+        let targetDir;
+        if (opts.to) {
+            targetDir = path.resolve(opts.to);
+        }
+        else {
+            const targetInput = await ask("\nTarget directory (where .gnosys/ should live)");
+            if (!targetInput) {
+                console.error("No target directory provided.");
+                rl?.close();
+                process.exit(1);
+            }
+            targetDir = path.resolve(targetInput);
+        }
+        // 3. Resolve name
+        const defaultName = opts.name || path.basename(targetDir);
+        const newName = opts.yes
+            ? defaultName
+            : await ask("Project name", defaultName);
+        // 4. Ask about sync and cleanup
+        let doSync = true;
+        let doDelete = true;
+        if (!opts.yes) {
+            const syncAnswer = await ask("\nSync memories to central DB?", "Y");
+            doSync = syncAnswer.toLowerCase() !== "n" && syncAnswer.toLowerCase() !== "no";
+            const deleteAnswer = await ask("Delete old .gnosys/ after migration?", "Y");
+            doDelete = deleteAnswer.toLowerCase() !== "n" && deleteAnswer.toLowerCase() !== "no";
+        }
+        // 5. Show summary and confirm
+        console.log("\n── Migration Summary ──");
+        console.log(`  From:       ${sourceDir}/.gnosys/`);
+        console.log(`  To:         ${targetDir}/.gnosys/`);
+        console.log(`  Name:       ${identity?.projectName || "(new)"} → ${newName}`);
+        console.log(`  Memories:   ${memFiles.length} files`);
+        console.log(`  Sync to DB: ${doSync ? "yes" : "no"}`);
+        console.log(`  Delete old: ${doDelete ? "yes" : "no"}`);
+        if (!opts.yes) {
+            const confirm = await ask("\nProceed?", "Y");
+            if (confirm.toLowerCase() === "n" || confirm.toLowerCase() === "no") {
+                console.log("Aborted.");
+                rl?.close();
+                return;
+            }
+        }
+        rl?.close();
+        // 6. Open central DB
+        let centralDb = null;
+        try {
+            centralDb = GnosysDB.openCentral();
+            if (!centralDb.isAvailable())
+                centralDb = null;
+        }
+        catch {
+            centralDb = null;
+        }
+        // 7. Run migration
+        console.log("\nMigrating...");
+        const result = await migrateProject({
+            sourcePath: sourceDir,
+            targetPath: targetDir,
+            newName,
+            deleteSource: doDelete,
+            centralDb: centralDb || undefined,
+        });
+        console.log(`  Copied ${result.memoryFileCount} memory files`);
+        console.log(`  Project: ${result.newIdentity.projectName} (${result.newIdentity.projectId})`);
+        console.log(`  Path:    ${result.newIdentity.workingDirectory}`);
+        console.log(`  Central DB: ${centralDb ? "updated ✓" : "not available"}`);
+        // 8. Sync memories to central DB
+        if (doSync && centralDb) {
+            console.log("\nSyncing memories to central DB...");
+            const matter = (await import("gray-matter")).default;
+            const { syncMemoryToDb } = await import("./lib/dbWrite.js");
+            const newStorePath = path.join(targetDir, ".gnosys");
+            const mdFiles = await glob("**/*.md", {
+                cwd: newStorePath,
+                ignore: ["**/CHANGELOG.md", "**/MANIFEST.md", "**/.git/**", "**/.obsidian/**"],
+            });
+            let synced = 0;
+            for (const file of mdFiles) {
+                try {
+                    const filePath = path.join(newStorePath, file);
+                    const raw = await fs.readFile(filePath, "utf-8");
+                    const parsed = matter(raw);
+                    if (parsed.data?.id) {
+                        syncMemoryToDb(centralDb, parsed.data, parsed.content, filePath, result.newIdentity.projectId, "project");
+                        synced++;
+                    }
+                }
+                catch {
+                    // Skip files that fail to parse
+                }
+            }
+            console.log(`  Synced ${synced} memories to central DB`);
+        }
+        if (centralDb)
+            centralDb.close();
+        if (doDelete) {
+            console.log(`\nOld .gnosys/ at ${sourceDir} removed.`);
+        }
+        console.log(`\nMigration complete! Run 'gnosys projects' to verify.`);
+    }
+    catch (err) {
+        rl?.close();
+        const msg = err instanceof Error ? err.message : String(err);
+        console.error(`\nMigration failed: ${msg}`);
+        process.exit(1);
+    }
+});
 // ─── gnosys stale ───────────────────────────────────────────────────────
 program
     .command("stale")
@@ -649,30 +823,34 @@ program
     const fullContent = opts.content
         ? `# ${opts.title || memory.frontmatter.title}\n\n${opts.content}`
         : undefined;
-    const updated = await sourceStore.store.updateMemory(memory.relativePath, updates, fullContent);
-    if (!updated) {
-        console.error(`Failed to update: ${memPath}`);
+    const memoryId = memory.frontmatter.id;
+    if (!memoryId) {
+        console.error(`Memory has no ID: ${memPath}`);
         process.exit(1);
     }
-    // Supersession cross-linking
-    if (opts.supersedes && updated.frontmatter.id) {
-        const allMemories = await resolver.getAllMemories();
-        const supersededMemory = allMemories.find((m) => m.frontmatter.id === opts.supersedes);
-        if (supersededMemory) {
-            const supersededStore = resolver
-                .getStores()
-                .find((s) => s.label === supersededMemory.sourceLabel);
-            if (supersededStore?.writable) {
-                await supersededStore.store.updateMemory(supersededMemory.relativePath, { superseded_by: updated.frontmatter.id, status: "superseded" });
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        const { syncUpdateToDb } = await import("./lib/dbWrite.js");
+        syncUpdateToDb(centralDb, memoryId, updates, fullContent);
+        // Supersession cross-linking
+        if (opts.supersedes && memoryId) {
+            const allMemories = await resolver.getAllMemories();
+            const supersededMemory = allMemories.find((m) => m.frontmatter.id === opts.supersedes);
+            if (supersededMemory) {
+                syncUpdateToDb(centralDb, supersededMemory.frontmatter.id, { superseded_by: memoryId, status: "superseded" });
                 console.log(`Cross-linked: ${supersededMemory.frontmatter.title} marked as superseded.`);
             }
         }
     }
+    finally {
+        centralDb?.close();
+    }
     const changedFields = Object.keys(updates);
     if (opts.content)
         changedFields.push("content");
-    console.log(`Memory updated: ${updated.frontmatter.title}`);
-    console.log(`Path: ${memory.sourceLabel}:${memory.relativePath}`);
+    console.log(`Memory updated: ${opts.title || memory.frontmatter.title}`);
+    console.log(`ID: ${memoryId}`);
     console.log(`Changed: ${changedFields.join(", ")}`);
 });
 // ─── gnosys reinforce <memoryId> ────────────────────────────────────────
@@ -701,17 +879,16 @@ program
     await fs.appendFile(logPath, entry + "\n", "utf-8");
     // If 'useful', update the memory's modified date (reset decay)
     if (opts.signal === "useful") {
-        const allMemories = await resolver.getAllMemories();
-        const memory = allMemories.find((m) => m.frontmatter.id === memoryId);
-        if (memory) {
-            const sourceStore = resolver
-                .getStores()
-                .find((s) => s.label === memory.sourceLabel);
-            if (sourceStore?.writable) {
-                await sourceStore.store.updateMemory(memory.relativePath, {
-                    modified: new Date().toISOString().split("T")[0],
-                });
-            }
+        let centralDb = null;
+        try {
+            centralDb = GnosysDB.openCentral();
+            const { syncUpdateToDb } = await import("./lib/dbWrite.js");
+            syncUpdateToDb(centralDb, memoryId, {
+                modified: new Date().toISOString().split("T")[0],
+            });
+        }
+        finally {
+            centralDb?.close();
         }
     }
     const messages = {
@@ -787,13 +964,7 @@ program
             centralDb?.close();
         }
     }
-    // ─── Default: file-based store (original behavior) ────────────
-    const resolver = await getResolver();
-    const writeTarget = resolver.getWriteTarget(opts.store || undefined);
-    if (!writeTarget) {
-        console.error("No writable store found.");
-        process.exit(1);
-    }
+    // ─── DB-only write ────────────────────────────────────────────
     let tags;
     try {
         tags = JSON.parse(opts.tags);
@@ -802,32 +973,47 @@ program
         console.error("Invalid --tags JSON. Example: '{\"domain\":[\"auth\"],\"type\":[\"decision\"]}'");
         process.exit(1);
     }
-    const id = await writeTarget.store.generateId(opts.category);
-    const slug = opts.title
-        .toLowerCase()
-        .replace(/[^a-z0-9]+/g, "-")
-        .replace(/^-|-$/g, "")
-        .substring(0, 60);
-    const today = new Date().toISOString().split("T")[0];
-    const frontmatter = {
-        id,
-        title: opts.title,
-        category: opts.category,
-        tags,
-        relevance: opts.relevance,
-        author: opts.author,
-        authority: opts.authority,
-        confidence: parseFloat(opts.confidence),
-        created: today,
-        modified: today,
-        last_reviewed: today,
-        status: "active",
-        supersedes: null,
-    };
-    const content = `# ${opts.title}\n\n${opts.content}`;
-    const relPath = await writeTarget.store.writeMemory(opts.category, `${slug}.md`, frontmatter, content);
-    console.log(`Memory added to [${writeTarget.label}]: ${opts.title}`);
-    console.log(`Path: ${writeTarget.label}:${relPath}`);
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        const projectId = await resolveProjectId();
+        const id = centralDb.getNextId(opts.category, projectId || undefined);
+        const now = new Date().toISOString();
+        const content = `# ${opts.title}\n\n${opts.content}`;
+        const tagsJson = Array.isArray(tags)
+            ? JSON.stringify(tags)
+            : JSON.stringify(Object.values(tags).flat());
+        centralDb.insertMemory({
+            id,
+            title: opts.title,
+            category: opts.category,
+            content,
+            summary: null,
+            tags: tagsJson,
+            relevance: opts.relevance || opts.content.slice(0, 200),
+            author: opts.author,
+            authority: opts.authority,
+            confidence: parseFloat(opts.confidence),
+            reinforcement_count: 0,
+            content_hash: "",
+            status: "active",
+            tier: "active",
+            supersedes: null,
+            superseded_by: null,
+            last_reinforced: null,
+            created: now,
+            modified: now,
+            embedding: null,
+            source_path: null,
+            project_id: projectId,
+            scope: "project",
+        });
+        console.log(`Memory added: ${opts.title}`);
+        console.log(`ID: ${id}`);
+    }
+    finally {
+        centralDb?.close();
+    }
 });
 // ─── gnosys ingest <file> ─────────────────────────────────────────────────
 program
@@ -1029,49 +1215,70 @@ Output ONLY the JSON array, no markdown fences.`,
     // Step 2: Check novelty and commit
     let added = 0;
     let skipped = 0;
-    for (const candidate of candidates) {
-        const searchTerms = candidate.search_terms.join(" ");
-        const existing = search.discover(searchTerms, 3);
-        if (existing.length > 0) {
-            console.log(`  ⏭ SKIP: "${candidate.summary}"`);
-            console.log(`    Overlaps with: ${existing[0].title}`);
-            skipped++;
-        }
-        else if (opts.dryRun) {
-            console.log(`  ➕ WOULD ADD: "${candidate.summary}" [${candidate.type}]`);
-            added++;
-        }
-        else {
-            try {
-                const result = await ingestion.ingest(candidate.summary);
-                const id = await writeTarget.store.generateId(result.category);
-                const today = new Date().toISOString().split("T")[0];
-                const frontmatter = {
-                    id,
-                    title: result.title,
-                    category: result.category,
-                    tags: result.tags,
-                    relevance: result.relevance,
-                    author: "ai",
-                    authority: "observed",
-                    confidence: result.confidence,
-                    created: today,
-                    modified: today,
-                    last_reviewed: today,
-                    status: "active",
-                    supersedes: null,
-                };
-                const content = `# ${result.title}\n\n${result.content}`;
-                const relPath = await writeTarget.store.writeMemory(result.category, `${result.filename}.md`, frontmatter, content);
-                console.log(`  ➕ ADDED: "${result.title}"`);
-                console.log(`    Path: ${writeTarget.label}:${relPath}`);
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        const projectId = await resolveProjectId();
+        for (const candidate of candidates) {
+            const searchTerms = candidate.search_terms.join(" ");
+            const existing = search.discover(searchTerms, 3);
+            if (existing.length > 0) {
+                console.log(`  ⏭ SKIP: "${candidate.summary}"`);
+                console.log(`    Overlaps with: ${existing[0].title}`);
+                skipped++;
+            }
+            else if (opts.dryRun) {
+                console.log(`  ➕ WOULD ADD: "${candidate.summary}" [${candidate.type}]`);
                 added++;
             }
-            catch (err) {
-                console.error(`  ❌ FAILED: "${candidate.summary}": ${err instanceof Error ? err.message : String(err)}`);
+            else {
+                try {
+                    const result = await ingestion.ingest(candidate.summary);
+                    const id = centralDb.getNextId(result.category, projectId || undefined);
+                    const now = new Date().toISOString();
+                    const content = `# ${result.title}\n\n${result.content}`;
+                    const resultTags = result.tags;
+                    const tagsJson = Array.isArray(resultTags)
+                        ? JSON.stringify(resultTags)
+                        : JSON.stringify(Object.values(resultTags).flat());
+                    centralDb.insertMemory({
+                        id,
+                        title: result.title,
+                        category: result.category,
+                        content,
+                        summary: null,
+                        tags: tagsJson,
+                        relevance: result.relevance,
+                        author: "ai",
+                        authority: "observed",
+                        confidence: result.confidence,
+                        reinforcement_count: 0,
+                        content_hash: "",
+                        status: "active",
+                        tier: "active",
+                        supersedes: null,
+                        superseded_by: null,
+                        last_reinforced: null,
+                        created: now,
+                        modified: now,
+                        embedding: null,
+                        source_path: null,
+                        project_id: projectId,
+                        scope: "project",
+                    });
+                    console.log(`  ➕ ADDED: "${result.title}"`);
+                    console.log(`    ID: ${id}`);
+                    added++;
+                }
+                catch (err) {
+                    console.error(`  ❌ FAILED: "${candidate.summary}": ${err instanceof Error ? err.message : String(err)}`);
+                }
             }
+            console.log();
         }
-        console.log();
+    }
+    finally {
+        centralDb?.close();
     }
     search.close();
     const mode = opts.dryRun ? "DRY RUN" : "COMMITTED";
@@ -2833,10 +3040,10 @@ program
         process.exit(1);
     }
 });
-// ─── gnosys migrate --to-central ────────────────────────────────────────
+// ─── gnosys migrate-db ──────────────────────────────────────────────────
 program
-    .command("migrate")
-    .description("Migrate data. Use --to-central to move per-project stores into the central DB.")
+    .command("migrate-db")
+    .description("Legacy data migration. Use --to-central to move per-project stores into the central DB.")
     .option("--to-central", "Migrate all discovered per-project stores into ~/.gnosys/gnosys.db")
     .option("-v, --verbose", "Verbose output")
     .action(async (opts) => {