gnosys 4.0.0

package/dist/lib/migrate.js

@@ -0,0 +1,260 @@
+/**
+ * Gnosys Migrate — Moves data from v1.x (Markdown + archive.db + embeddings.db)
+ * into the unified gnosys.db (v2.0).
+ *
+ * Safe: original .md files and old DBs are untouched.
+ * Reversible: delete gnosys.db to revert.
+ */
+import path from "path";
+import { GnosysDB, fnv1a } from "./db.js";
+import { GnosysStore } from "./store.js";
+import { GnosysArchive } from "./archive.js";
+// Dynamic import for embeddings DB
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+let Database = null;
+try {
+    Database = (await import("better-sqlite3")).default;
+}
+catch {
+    // Not available
+}
+/**
+ * Extract [[wikilinks]] from markdown content.
+ * Returns array of link targets (the text inside double brackets).
+ */
+function extractWikilinks(content) {
+    const re = /\[\[([^\]]+)\]\]/g;
+    const links = [];
+    let match;
+    while ((match = re.exec(content)) !== null) {
+        links.push(match[1]);
+    }
+    return links;
+}
+/**
+ * Resolve a wikilink target to a memory ID using fuzzy title matching.
+ */
+function resolveWikilink(target, titleMap) {
+    // Exact match on title
+    const lower = target.toLowerCase().replace(/\.md$/, "");
+    for (const [title, id] of titleMap) {
+        if (title.toLowerCase() === lower)
+            return id;
+    }
+    // Partial match
+    for (const [title, id] of titleMap) {
+        if (title.toLowerCase().includes(lower) || lower.includes(title.toLowerCase()))
+            return id;
+    }
+    return null;
+}
+/**
+ * Migrate all data from v1.x format into gnosys.db.
+ */
+export async function migrate(storePath, options) {
+    const log = options?.verbose ? console.log : () => { };
+    const stats = {
+        memoriesMigrated: 0,
+        archiveMigrated: 0,
+        relationshipsCreated: 0,
+        ftsBuild: false,
+    };
+    // 1. Open/create gnosys.db
+    const db = new GnosysDB(storePath);
+    if (!db.isAvailable()) {
+        throw new Error("Cannot create gnosys.db — better-sqlite3 not available");
+    }
+    // 2. Read all active .md memories
+    const store = new GnosysStore(storePath);
+    await store.init();
+    const memories = await store.getAllMemories();
+    log(`Found ${memories.length} active memories to migrate`);
+    // Build title→ID map for wikilink resolution
+    const titleMap = new Map();
+    // 3. Insert active memories
+    db.transaction(() => {
+        for (const mem of memories) {
+            const tags = Array.isArray(mem.frontmatter.tags)
+                ? JSON.stringify(mem.frontmatter.tags)
+                : JSON.stringify(Object.values(mem.frontmatter.tags).flat());
+            const contentHash = fnv1a(mem.content);
+            db.insertMemory({
+                id: mem.frontmatter.id,
+                title: mem.frontmatter.title,
+                category: mem.frontmatter.category,
+                content: mem.content,
+                summary: null,
+                tags,
+                relevance: mem.frontmatter.relevance || "",
+                author: mem.frontmatter.author || "ai",
+                authority: mem.frontmatter.authority || "imported",
+                confidence: mem.frontmatter.confidence ?? 0.8,
+                reinforcement_count: mem.frontmatter.reinforcement_count || 0,
+                content_hash: contentHash,
+                status: mem.frontmatter.status || "active",
+                tier: "active",
+                supersedes: mem.frontmatter.supersedes || null,
+                superseded_by: mem.frontmatter.superseded_by || null,
+                last_reinforced: mem.frontmatter.last_reinforced || null,
+                created: mem.frontmatter.created,
+                modified: mem.frontmatter.modified,
+                embedding: null,
+                source_path: mem.relativePath,
+                project_id: null,
+                scope: "project",
+            });
+            titleMap.set(mem.frontmatter.title, mem.frontmatter.id);
+            stats.memoriesMigrated++;
+        }
+    });
+    log(`Migrated ${stats.memoriesMigrated} active memories`);
+    // 4. Migrate archive.db entries
+    try {
+        const archive = new GnosysArchive(storePath);
+        if (archive.isAvailable()) {
+            const archiveIds = archive.getAllArchivedIds();
+            log(`Found ${archiveIds.length} archived memories to migrate`);
+            db.transaction(() => {
+                for (const archiveId of archiveIds) {
+                    const row = archive.getArchivedMemory(archiveId);
+                    if (!row)
+                        continue;
+                    // Parse stored frontmatter
+                    let frontmatter = {};
+                    try {
+                        frontmatter = JSON.parse(row.yaml_frontmatter);
+                    }
+                    catch {
+                        // Use minimal fields from row
+                    }
+                    const contentHash = fnv1a(row.content);
+                    db.insertMemory({
+                        id: row.id,
+                        title: row.title,
+                        category: row.category,
+                        content: row.content,
+                        summary: null,
+                        tags: row.tags ? JSON.stringify(row.tags.split(" ").filter(Boolean)) : "[]",
+                        relevance: frontmatter.relevance || row.tags || "",
+                        author: frontmatter.author || "ai",
+                        authority: frontmatter.authority || "imported",
+                        confidence: row.confidence ?? 0.8,
+                        reinforcement_count: frontmatter.reinforcement_count || 0,
+                        content_hash: contentHash,
+                        status: "archived",
+                        tier: "archive",
+                        supersedes: frontmatter.supersedes || null,
+                        superseded_by: frontmatter.superseded_by || null,
+                        last_reinforced: row.last_reinforced || null,
+                        created: frontmatter.created || row.archived_date,
+                        modified: frontmatter.modified || row.archived_date,
+                        embedding: null,
+                        source_path: row.original_path,
+                        project_id: null,
+                        scope: "project",
+                    });
+                    titleMap.set(row.title, row.id);
+                    stats.archiveMigrated++;
+                }
+            });
+            archive.close();
+            log(`Migrated ${stats.archiveMigrated} archived memories`);
+        }
+    }
+    catch {
+        log("No archive.db found or archive migration skipped");
+    }
+    // 5. Copy embeddings from embeddings.db
+    try {
+        const embPath = path.join(storePath, ".config", "embeddings.db");
+        if (Database) {
+            const embDb = new Database(embPath, { readonly: true });
+            const rows = embDb.prepare("SELECT file_path, embedding FROM embeddings").all();
+            let embCount = 0;
+            for (const row of rows) {
+                // file_path might be "category/file.md" — we need to find the matching memory
+                const matchingMemory = memories.find((m) => m.relativePath === row.file_path);
+                if (matchingMemory) {
+                    db.updateEmbedding(matchingMemory.frontmatter.id, row.embedding);
+                    embCount++;
+                }
+            }
+            embDb.close();
+            log(`Copied ${embCount} embeddings`);
+        }
+    }
+    catch {
+        log("No embeddings.db found or embedding copy skipped");
+    }
+    // 6. Build relationships from wikilinks
+    const today = new Date().toISOString().split("T")[0];
+    db.transaction(() => {
+        for (const mem of memories) {
+            const links = extractWikilinks(mem.content);
+            for (const link of links) {
+                const targetId = resolveWikilink(link, titleMap);
+                if (targetId && targetId !== mem.frontmatter.id) {
+                    db.insertRelationship({
+                        source_id: mem.frontmatter.id,
+                        target_id: targetId,
+                        rel_type: "references",
+                        label: link,
+                        confidence: 1.0,
+                        created: today,
+                    });
+                    stats.relationshipsCreated++;
+                }
+            }
+            // Build supersedes relationships
+            if (mem.frontmatter.supersedes) {
+                const supersedesIds = mem.frontmatter.supersedes.split(",").map((s) => s.trim());
+                for (const sid of supersedesIds) {
+                    if (sid) {
+                        db.insertRelationship({
+                            source_id: mem.frontmatter.id,
+                            target_id: sid,
+                            rel_type: "supersedes",
+                            label: null,
+                            confidence: 1.0,
+                            created: today,
+                        });
+                        stats.relationshipsCreated++;
+                    }
+                }
+            }
+        }
+    });
+    log(`Created ${stats.relationshipsCreated} relationships`);
+    // 7. Log migration in audit
+    db.logAudit({
+        timestamp: new Date().toISOString(),
+        operation: "migrate",
+        memory_id: null,
+        details: JSON.stringify(stats),
+        duration_ms: null,
+        trace_id: null,
+    });
+    stats.ftsBuild = true;
+    db.close();
+    return stats;
+}
+/**
+ * Format migration results for CLI output.
+ */
+export function formatMigrationReport(stats) {
+    const lines = [
+        "╔════════════════════════════════════════╗",
+        "║     Gnosys Migration Complete          ║",
+        "╚════════════════════════════════════════╝",
+        "",
+        `  Active memories migrated:   ${stats.memoriesMigrated}`,
+        `  Archived memories migrated: ${stats.archiveMigrated}`,
+        `  Relationships created:      ${stats.relationshipsCreated}`,
+        `  FTS5 index built:           ${stats.ftsBuild ? "✓" : "✗"}`,
+        "",
+        "  Original .md files and archive.db are untouched.",
+        "  Delete gnosys.db to revert to v1.x format.",
+    ];
+    return lines.join("\n");
+}
+//# sourceMappingURL=migrate.js.map

package/dist/lib/migrate.js.map

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package/dist/lib/preferences.d.ts

@@ -0,0 +1,49 @@
+/**
+ * Gnosys Preferences — Phase 8b.
+ *
+ * User preferences stored as regular Gnosys memories in the central DB
+ * with scope='user' and category='preferences'. The memory system IS
+ * the config system.
+ *
+ * Preferences have a `key` (stored in the memory id as `pref-<key>`)
+ * and a `value` (stored in content). They're searchable, decayable,
+ * and versioned just like any other memory.
+ */
+import { GnosysDB } from "./db.js";
+export interface Preference {
+    key: string;
+    value: string;
+    title: string;
+    tags: string[];
+    confidence: number;
+    created: string;
+    modified: string;
+}
+/** Well-known preference keys used by the rules generator */
+export declare const KNOWN_PREFERENCE_KEYS: readonly ["commit-convention", "code-style", "llm-provider", "agent-behavior", "testing-approach", "documentation-style", "naming-convention", "error-handling", "review-process", "deploy-workflow"];
+/**
+ * Set a user preference. Creates or updates a memory in the central DB
+ * with scope='user' and category='preferences'.
+ */
+export declare function setPreference(db: GnosysDB, key: string, value: string, opts?: {
+    title?: string;
+    tags?: string[];
+    confidence?: number;
+}): Preference;
+/**
+ * Get a single preference by key.
+ */
+export declare function getPreference(db: GnosysDB, key: string): Preference | null;
+/**
+ * Get all user preferences.
+ */
+export declare function getAllPreferences(db: GnosysDB): Preference[];
+/**
+ * Delete a preference by key.
+ */
+export declare function deletePreference(db: GnosysDB, key: string): boolean;
+/**
+ * Search preferences by keyword.
+ */
+export declare function searchPreferences(db: GnosysDB, query: string): Preference[];
+//# sourceMappingURL=preferences.d.ts.map

package/dist/lib/preferences.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"preferences.d.ts","sourceRoot":"","sources":["../../src/lib/preferences.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,QAAQ,EAAmB,MAAM,SAAS,CAAC;AAIpD,MAAM,WAAW,UAAU;IACzB,GAAG,EAAE,MAAM,CAAC;IACZ,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,6DAA6D;AAC7D,eAAO,MAAM,qBAAqB,uMAWxB,CAAC;AAIX;;;GAGG;AACH,wBAAgB,aAAa,CAC3B,EAAE,EAAE,QAAQ,EACZ,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EACb,IAAI,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,CAAA;CAAE,GAC9D,UAAU,CA4CZ;AAED;;GAEG;AACH,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI,CAK1E;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,GAAG,UAAU,EAAE,CAK5D;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,GAAG,OAAO,CAMnE;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,MAAM,GAAG,UAAU,EAAE,CAU3E"}

package/dist/lib/preferences.js

@@ -0,0 +1,149 @@
+/**
+ * Gnosys Preferences — Phase 8b.
+ *
+ * User preferences stored as regular Gnosys memories in the central DB
+ * with scope='user' and category='preferences'. The memory system IS
+ * the config system.
+ *
+ * Preferences have a `key` (stored in the memory id as `pref-<key>`)
+ * and a `value` (stored in content). They're searchable, decayable,
+ * and versioned just like any other memory.
+ */
+import { fnv1a } from "./db.js";
+/** Well-known preference keys used by the rules generator */
+export const KNOWN_PREFERENCE_KEYS = [
+    "commit-convention",
+    "code-style",
+    "llm-provider",
+    "agent-behavior",
+    "testing-approach",
+    "documentation-style",
+    "naming-convention",
+    "error-handling",
+    "review-process",
+    "deploy-workflow",
+];
+// ─── Preference CRUD ────────────────────────────────────────────────────
+/**
+ * Set a user preference. Creates or updates a memory in the central DB
+ * with scope='user' and category='preferences'.
+ */
+export function setPreference(db, key, value, opts) {
+    const now = new Date().toISOString().split("T")[0];
+    const id = `pref-${key}`;
+    const title = opts?.title || formatPreferenceTitle(key);
+    const tags = opts?.tags || [];
+    const confidence = opts?.confidence ?? 0.95;
+    // Check if it already exists
+    const existing = db.getMemory(id);
+    db.insertMemory({
+        id,
+        title,
+        category: "preferences",
+        content: `# ${title}\n\n${value}`,
+        summary: value.length > 200 ? value.substring(0, 200) + "..." : value,
+        tags: JSON.stringify(tags),
+        relevance: `preference ${key} user-preference ${tags.join(" ")}`,
+        author: "human",
+        authority: "declared",
+        confidence,
+        reinforcement_count: existing ? (existing.reinforcement_count + 1) : 0,
+        content_hash: fnv1a(value),
+        status: "active",
+        tier: "active",
+        supersedes: null,
+        superseded_by: null,
+        last_reinforced: existing ? now : null,
+        created: existing?.created || now,
+        modified: now,
+        source_path: null,
+        project_id: null, // user-level, not project-scoped
+        scope: "user",
+    });
+    return {
+        key,
+        value,
+        title,
+        tags,
+        confidence,
+        created: existing?.created || now,
+        modified: now,
+    };
+}
+/**
+ * Get a single preference by key.
+ */
+export function getPreference(db, key) {
+    const id = `pref-${key}`;
+    const mem = db.getMemory(id);
+    if (!mem || mem.category !== "preferences")
+        return null;
+    return memoryToPreference(mem);
+}
+/**
+ * Get all user preferences.
+ */
+export function getAllPreferences(db) {
+    const mems = db.getMemoriesByScope("user");
+    return mems
+        .filter((m) => m.category === "preferences" && m.status === "active")
+        .map(memoryToPreference);
+}
+/**
+ * Delete a preference by key.
+ */
+export function deletePreference(db, key) {
+    const id = `pref-${key}`;
+    const mem = db.getMemory(id);
+    if (!mem || mem.category !== "preferences")
+        return false;
+    db.deleteMemory(id);
+    return true;
+}
+/**
+ * Search preferences by keyword.
+ */
+export function searchPreferences(db, query) {
+    const results = db.searchFts(`preferences ${query}`, 20);
+    const prefs = [];
+    for (const r of results) {
+        if (r.id.startsWith("pref-")) {
+            const mem = db.getMemory(r.id);
+            if (mem)
+                prefs.push(memoryToPreference(mem));
+        }
+    }
+    return prefs;
+}
+// ─── Helpers ────────────────────────────────────────────────────────────
+function memoryToPreference(mem) {
+    // Extract value from content (strip "# Title\n\n" prefix)
+    const content = mem.content;
+    const lines = content.split("\n");
+    const valueStart = lines[0].startsWith("# ") ? 2 : 0;
+    const value = lines.slice(valueStart).join("\n").trim();
+    let tags = [];
+    try {
+        const parsed = JSON.parse(mem.tags);
+        tags = Array.isArray(parsed) ? parsed : Object.values(parsed).flat();
+    }
+    catch {
+        tags = [];
+    }
+    return {
+        key: mem.id.replace(/^pref-/, ""),
+        value,
+        title: mem.title,
+        tags,
+        confidence: mem.confidence,
+        created: mem.created,
+        modified: mem.modified,
+    };
+}
+function formatPreferenceTitle(key) {
+    return key
+        .split("-")
+        .map((w) => w.charAt(0).toUpperCase() + w.slice(1))
+        .join(" ");
+}
+//# sourceMappingURL=preferences.js.map

package/dist/lib/preferences.js.map

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package/dist/lib/projectIdentity.d.ts

@@ -0,0 +1,66 @@
+/**
+ * Gnosys Project Identity — v3.0 Centralized Brain.
+ *
+ * Each project has a .gnosys/gnosys.json that stores its identity:
+ *   projectId, projectName, workingDirectory, user, agentRulesTarget, obsidianVault
+ *
+ * The central DB (~/.gnosys/gnosys.db) mirrors this in the `projects` table.
+ * gnosys init creates both the local identity file AND the central DB record.
+ */
+import { GnosysDB } from "./db.js";
+/** Shape of .gnosys/gnosys.json (project identity) */
+export interface ProjectIdentity {
+    projectId: string;
+    projectName: string;
+    workingDirectory: string;
+    user: string;
+    agentRulesTarget: string | null;
+    obsidianVault: string | null;
+    createdAt: string;
+    schemaVersion: number;
+}
+/**
+ * Detect which agent IDE is being used.
+ * Returns the appropriate rules file target path.
+ */
+export declare function detectAgentRulesTarget(projectDir: string): string | null;
+/**
+ * Read project identity from .gnosys/gnosys.json.
+ * Returns null if file doesn't exist or is invalid.
+ */
+export declare function readProjectIdentity(projectDir: string): Promise<ProjectIdentity | null>;
+/**
+ * Write project identity to .gnosys/gnosys.json.
+ */
+export declare function writeProjectIdentity(projectDir: string, identity: ProjectIdentity): Promise<void>;
+/**
+ * Create a new project identity.
+ * Generates UUID, detects IDE, writes local file, registers in central DB.
+ */
+export declare function createProjectIdentity(projectDir: string, opts?: {
+    projectName?: string;
+    centralDb?: GnosysDB;
+}): Promise<ProjectIdentity>;
+/**
+ * Check if the working directory has changed since last init.
+ * Returns the identity if a mismatch is detected (needs re-init).
+ */
+export declare function checkDirectoryMismatch(projectDir: string): Promise<{
+    mismatch: boolean;
+    identity: ProjectIdentity | null;
+    currentDir: string;
+}>;
+/**
+ * Update the working directory in both local identity and central DB.
+ * Called when a directory move is detected.
+ */
+export declare function updateWorkingDirectory(projectDir: string, centralDb?: GnosysDB): Promise<ProjectIdentity | null>;
+/**
+ * Find the project identity by walking up from a directory.
+ * Returns the identity and project root directory if found.
+ */
+export declare function findProjectIdentity(startDir: string): Promise<{
+    identity: ProjectIdentity;
+    projectRoot: string;
+} | null>;
+//# sourceMappingURL=projectIdentity.d.ts.map

package/dist/lib/projectIdentity.d.ts.map

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