gnosys 4.0.0

package/dist/lib/projectIdentity.js

@@ -0,0 +1,148 @@
+/**
+ * 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 fs from "fs/promises";
+import fsSync from "fs";
+import path from "path";
+import crypto from "crypto";
+import os from "os";
+const IDENTITY_SCHEMA_VERSION = 1;
+/**
+ * Detect which agent IDE is being used.
+ * Returns the appropriate rules file target path.
+ */
+export function detectAgentRulesTarget(projectDir) {
+    // Check for Cursor
+    if (fsSync.existsSync(path.join(projectDir, ".cursor"))) {
+        return ".cursor/rules/gnosys.mdc";
+    }
+    // Check for Claude Code
+    if (fsSync.existsSync(path.join(projectDir, "CLAUDE.md"))) {
+        return "CLAUDE.md";
+    }
+    return null;
+}
+/**
+ * Read project identity from .gnosys/gnosys.json.
+ * Returns null if file doesn't exist or is invalid.
+ */
+export async function readProjectIdentity(projectDir) {
+    const identityPath = path.join(projectDir, ".gnosys", "gnosys.json");
+    try {
+        const raw = await fs.readFile(identityPath, "utf-8");
+        const parsed = JSON.parse(raw);
+        // Validate required fields
+        if (!parsed.projectId || !parsed.projectName || !parsed.workingDirectory) {
+            return null;
+        }
+        return parsed;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Write project identity to .gnosys/gnosys.json.
+ */
+export async function writeProjectIdentity(projectDir, identity) {
+    const identityPath = path.join(projectDir, ".gnosys", "gnosys.json");
+    await fs.writeFile(identityPath, JSON.stringify(identity, null, 2) + "\n", "utf-8");
+}
+/**
+ * Create a new project identity.
+ * Generates UUID, detects IDE, writes local file, registers in central DB.
+ */
+export async function createProjectIdentity(projectDir, opts) {
+    const resolvedDir = path.resolve(projectDir);
+    const projectName = opts?.projectName || path.basename(resolvedDir);
+    const user = os.userInfo().username || "unknown";
+    const now = new Date().toISOString();
+    // Check if identity already exists and reuse the projectId
+    const existing = await readProjectIdentity(resolvedDir);
+    const identity = {
+        projectId: existing?.projectId || crypto.randomUUID(),
+        projectName,
+        workingDirectory: resolvedDir,
+        user,
+        agentRulesTarget: detectAgentRulesTarget(resolvedDir),
+        obsidianVault: ".gnosys/vault",
+        createdAt: existing?.createdAt || now,
+        schemaVersion: IDENTITY_SCHEMA_VERSION,
+    };
+    // Write local identity file
+    await writeProjectIdentity(resolvedDir, identity);
+    // Register in central DB if available
+    if (opts?.centralDb?.isAvailable()) {
+        const dbProject = {
+            id: identity.projectId,
+            name: identity.projectName,
+            working_directory: identity.workingDirectory,
+            user: identity.user,
+            agent_rules_target: identity.agentRulesTarget,
+            obsidian_vault: identity.obsidianVault
+                ? path.join(identity.workingDirectory, identity.obsidianVault)
+                : null,
+            created: identity.createdAt,
+            modified: now,
+        };
+        opts.centralDb.insertProject(dbProject);
+    }
+    return identity;
+}
+/**
+ * Check if the working directory has changed since last init.
+ * Returns the identity if a mismatch is detected (needs re-init).
+ */
+export async function checkDirectoryMismatch(projectDir) {
+    const resolvedDir = path.resolve(projectDir);
+    const identity = await readProjectIdentity(resolvedDir);
+    if (!identity) {
+        return { mismatch: false, identity: null, currentDir: resolvedDir };
+    }
+    const mismatch = identity.workingDirectory !== resolvedDir;
+    return { mismatch, identity, currentDir: resolvedDir };
+}
+/**
+ * Update the working directory in both local identity and central DB.
+ * Called when a directory move is detected.
+ */
+export async function updateWorkingDirectory(projectDir, centralDb) {
+    const resolvedDir = path.resolve(projectDir);
+    const identity = await readProjectIdentity(resolvedDir);
+    if (!identity)
+        return null;
+    // Update local file
+    identity.workingDirectory = resolvedDir;
+    await writeProjectIdentity(resolvedDir, identity);
+    // Update central DB
+    if (centralDb?.isAvailable()) {
+        centralDb.updateProject(identity.projectId, {
+            working_directory: resolvedDir,
+            modified: new Date().toISOString(),
+        });
+    }
+    return identity;
+}
+/**
+ * Find the project identity by walking up from a directory.
+ * Returns the identity and project root directory if found.
+ */
+export async function findProjectIdentity(startDir) {
+    let dir = path.resolve(startDir);
+    const root = path.parse(dir).root;
+    while (dir !== root) {
+        const identity = await readProjectIdentity(dir);
+        if (identity) {
+            return { identity, projectRoot: dir };
+        }
+        dir = path.dirname(dir);
+    }
+    return null;
+}
+//# sourceMappingURL=projectIdentity.js.map

package/dist/lib/projectIdentity.js.map

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package/dist/lib/recall.d.ts

@@ -0,0 +1,82 @@
+/**
+ * Gnosys Recall — Automatic memory injection via MCP Resource.
+ *
+ * The host (Cursor, Claude Desktop, Claude Code, Cowork) reads the
+ * gnosys://recall resource on every turn. This module runs the fast
+ * FTS5 lookup and returns a citation-heavy <gnosys-recall> block that
+ * gets injected into the model context automatically — no tool call needed.
+ *
+ * Pipeline: FTS5 keyword search → relevance scoring → aggressive/filtered
+ *           selection → archive fallback → format as [[wikilink]] block.
+ *
+ * Config (gnosys.json):
+ *   "recall": { "aggressive": true, "maxMemories": 8, "minRelevance": 0.4 }
+ *
+ * When aggressive=true (default): inject top memories even if relevance is
+ * medium. This boosts recall in long sessions where context drifts.
+ *
+ * v2.0: When GnosysDB is available, recall runs entirely from SQLite —
+ * no filesystem reads, no separate search.db. Pure DB lookup. Sub-10ms.
+ *
+ * No LLM calls. No embeddings. Pure index lookup. Sub-50ms.
+ */
+import { GnosysSearch } from "./search.js";
+import { GnosysResolver } from "./resolver.js";
+import { GnosysDB } from "./db.js";
+import { RecallConfig } from "./config.js";
+export interface RecallResult {
+    memories: RecallMemory[];
+    totalActive: number;
+    totalArchived: number;
+    recallTimeMs: number;
+    aggressive: boolean;
+}
+export interface RecallMemory {
+    id: string;
+    title: string;
+    category: string;
+    relevance: string;
+    confidence: number;
+    path: string;
+    fromArchive: boolean;
+    snippet: string;
+    /** Normalized relevance score (0-1, higher = more relevant) */
+    relevanceScore: number;
+}
+/**
+ * Fast recall — keyword search only, no LLM, no embeddings.
+ * Designed to run on every host turn via MCP Resource (sub-50ms target).
+ *
+ * v2.0: When gnosysDb is provided, recall runs entirely from SQLite.
+ * No filesystem reads. Sub-10ms.
+ *
+ * When aggressive=true (default):
+ *   - Always returns up to maxMemories regardless of relevance score
+ *   - Uses minRelevance as a soft floor, not a hard cutoff
+ *   - Injects even medium-relevance memories to boost context in long sessions
+ *
+ * When aggressive=false:
+ *   - Only returns memories above minRelevance threshold
+ *   - May return zero memories if nothing matches well
+ */
+export declare function recall(query: string, options: {
+    limit?: number;
+    search: GnosysSearch;
+    resolver: GnosysResolver;
+    storePath: string;
+    traceId?: string;
+    recallConfig?: RecallConfig;
+    /** v2.0: When provided, recall uses SQLite directly — no filesystem reads */
+    gnosysDb?: GnosysDB;
+}): Promise<RecallResult>;
+/**
+ * Format recall results as a host-friendly <gnosys-recall> block.
+ * This is what gets injected into the model context on every turn
+ * via the MCP Resource. Citation-heavy with [[wikilinks]].
+ */
+export declare function formatRecall(result: RecallResult): string;
+/**
+ * Format recall results as a concise CLI-friendly output.
+ */
+export declare function formatRecallCLI(result: RecallResult): string;
+//# sourceMappingURL=recall.d.ts.map

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

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package/dist/lib/recall.js

@@ -0,0 +1,289 @@
+/**
+ * Gnosys Recall — Automatic memory injection via MCP Resource.
+ *
+ * The host (Cursor, Claude Desktop, Claude Code, Cowork) reads the
+ * gnosys://recall resource on every turn. This module runs the fast
+ * FTS5 lookup and returns a citation-heavy <gnosys-recall> block that
+ * gets injected into the model context automatically — no tool call needed.
+ *
+ * Pipeline: FTS5 keyword search → relevance scoring → aggressive/filtered
+ *           selection → archive fallback → format as [[wikilink]] block.
+ *
+ * Config (gnosys.json):
+ *   "recall": { "aggressive": true, "maxMemories": 8, "minRelevance": 0.4 }
+ *
+ * When aggressive=true (default): inject top memories even if relevance is
+ * medium. This boosts recall in long sessions where context drifts.
+ *
+ * v2.0: When GnosysDB is available, recall runs entirely from SQLite —
+ * no filesystem reads, no separate search.db. Pure DB lookup. Sub-10ms.
+ *
+ * No LLM calls. No embeddings. Pure index lookup. Sub-50ms.
+ */
+import { GnosysArchive } from "./archive.js";
+import { auditLog } from "./audit.js";
+/** Default recall config */
+const DEFAULT_RECALL_CONFIG = {
+    aggressive: true,
+    maxMemories: 8,
+    minRelevance: 0.4,
+};
+/**
+ * Normalize FTS5 rank to a 0-1 relevance score.
+ * FTS5 rank is negative (closer to 0 = more relevant).
+ * We map it to 0-1 where 1 = most relevant.
+ */
+function normalizeRank(rank, allRanks) {
+    if (allRanks.length === 0)
+        return 0.5;
+    if (allRanks.length === 1)
+        return 0.9;
+    const minRank = Math.min(...allRanks); // Most relevant (most negative)
+    const maxRank = Math.max(...allRanks); // Least relevant
+    if (maxRank === minRank)
+        return 0.9;
+    // Linear normalization: most negative → 1.0, least negative → 0.3
+    return 0.3 + 0.7 * ((maxRank - rank) / (maxRank - minRank));
+}
+/**
+ * Fast recall — keyword search only, no LLM, no embeddings.
+ * Designed to run on every host turn via MCP Resource (sub-50ms target).
+ *
+ * v2.0: When gnosysDb is provided, recall runs entirely from SQLite.
+ * No filesystem reads. Sub-10ms.
+ *
+ * When aggressive=true (default):
+ *   - Always returns up to maxMemories regardless of relevance score
+ *   - Uses minRelevance as a soft floor, not a hard cutoff
+ *   - Injects even medium-relevance memories to boost context in long sessions
+ *
+ * When aggressive=false:
+ *   - Only returns memories above minRelevance threshold
+ *   - May return zero memories if nothing matches well
+ */
+export async function recall(query, options) {
+    const start = performance.now();
+    const cfg = options.recallConfig || DEFAULT_RECALL_CONFIG;
+    const limit = options.limit || cfg.maxMemories;
+    // ─── v2.0 DB-backed fast path ──────────────────────────────────────
+    if (options.gnosysDb?.isAvailable() && options.gnosysDb?.isMigrated()) {
+        return recallFromDb(query, options.gnosysDb, limit, cfg, options.traceId);
+    }
+    // ─── v1.x legacy path (filesystem + search.db) ────────────────────
+    const memories = [];
+    // Step 1: Fast keyword search on active memories (FTS5 — sub-10ms)
+    const fetchLimit = Math.max(limit * 2, 15);
+    const activeResults = options.search.discover(query, fetchLimit);
+    const allRanks = activeResults.map((r) => r.rank);
+    for (const r of activeResults) {
+        const memory = await options.resolver.readMemory(r.relative_path);
+        if (memory) {
+            const relevanceScore = normalizeRank(r.rank, allRanks);
+            memories.push({
+                id: memory.frontmatter.id,
+                title: memory.frontmatter.title,
+                category: memory.frontmatter.category,
+                relevance: memory.frontmatter.relevance || "",
+                confidence: memory.frontmatter.confidence,
+                path: r.relative_path,
+                fromArchive: false,
+                snippet: memory.content.substring(0, 300),
+                relevanceScore,
+            });
+        }
+    }
+    // Step 2: Archive fallback if active results are thin
+    let totalArchived = 0;
+    if (memories.length < limit) {
+        try {
+            const archive = new GnosysArchive(options.storePath);
+            if (archive.isAvailable()) {
+                const stats = archive.getStats();
+                totalArchived = stats.totalArchived;
+                const archiveResults = archive.searchArchive(query, limit - memories.length);
+                const existingTitles = new Set(memories.map((m) => m.title.toLowerCase()));
+                for (const ar of archiveResults) {
+                    if (!existingTitles.has(ar.title.toLowerCase())) {
+                        memories.push({
+                            id: ar.id,
+                            title: ar.title,
+                            category: ar.category,
+                            relevance: ar.tags,
+                            confidence: 0,
+                            path: `archive:${ar.category}/${ar.id}`,
+                            fromArchive: true,
+                            snippet: ar.snippet,
+                            relevanceScore: 0.5,
+                        });
+                    }
+                }
+                archive.close();
+            }
+        }
+        catch {
+            // Archive not available — degrade gracefully
+        }
+    }
+    // Step 3: Apply filtering
+    const result = applyRecallFiltering(memories, activeResults.length, totalArchived, limit, cfg, start);
+    auditLog({
+        operation: "recall",
+        query,
+        resultCount: result.memories.length,
+        durationMs: result.recallTimeMs,
+        traceId: options.traceId,
+        details: {
+            aggressive: cfg.aggressive,
+            totalCandidates: memories.length,
+            filtered: result.memories.length,
+        },
+    });
+    return result;
+}
+/**
+ * v2.0 DB-backed recall — runs entirely from gnosys.db.
+ * No filesystem reads. No separate search.db. Sub-10ms target.
+ */
+function recallFromDb(query, db, limit, cfg, traceId) {
+    const start = performance.now();
+    const memories = [];
+    // Step 1: FTS5 discover on gnosys.db
+    const fetchLimit = Math.max(limit * 2, 15);
+    const dbResults = db.discoverFts(query, fetchLimit);
+    const allRanks = dbResults.map((r) => r.rank);
+    for (const r of dbResults) {
+        const mem = db.getMemory(r.id);
+        if (mem && mem.tier === "active" && mem.status === "active") {
+            const relevanceScore = normalizeRank(r.rank, allRanks);
+            memories.push({
+                id: mem.id,
+                title: mem.title,
+                category: mem.category,
+                relevance: mem.relevance || "",
+                confidence: mem.confidence,
+                path: mem.id,
+                fromArchive: false,
+                snippet: mem.content.substring(0, 300),
+                relevanceScore,
+            });
+        }
+    }
+    // Step 2: Archive tier fallback if active results are thin
+    const counts = db.getMemoryCount();
+    if (memories.length < limit) {
+        for (const r of dbResults) {
+            if (memories.length >= limit)
+                break;
+            const mem = db.getMemory(r.id);
+            if (mem && mem.tier === "archive") {
+                const existingIds = new Set(memories.map((m) => m.id));
+                if (!existingIds.has(mem.id)) {
+                    const relevanceScore = normalizeRank(r.rank, allRanks);
+                    memories.push({
+                        id: mem.id,
+                        title: mem.title,
+                        category: mem.category,
+                        relevance: mem.relevance || "",
+                        confidence: mem.confidence,
+                        path: mem.id,
+                        fromArchive: true,
+                        snippet: mem.content.substring(0, 300),
+                        relevanceScore,
+                    });
+                }
+            }
+        }
+    }
+    // Step 3: Apply same filtering logic
+    const result = applyRecallFiltering(memories, dbResults.filter((r) => {
+        const m = db.getMemory(r.id);
+        return m && m.tier === "active";
+    }).length, counts.archived, limit, cfg, start);
+    // Audit via db instead of JSONL
+    db.logAudit({
+        timestamp: new Date().toISOString(),
+        operation: "recall",
+        memory_id: null,
+        details: JSON.stringify({
+            query,
+            aggressive: cfg.aggressive,
+            totalCandidates: memories.length,
+            filtered: result.memories.length,
+        }),
+        duration_ms: Math.round(result.recallTimeMs),
+        trace_id: traceId || null,
+    });
+    return result;
+}
+/**
+ * Shared filtering logic for both v1.x and v2.0 paths.
+ */
+function applyRecallFiltering(memories, totalActive, totalArchived, limit, cfg, startTime) {
+    const sorted = [...memories].sort((a, b) => b.relevanceScore - a.relevanceScore);
+    let filtered;
+    if (cfg.aggressive) {
+        const guaranteed = sorted.slice(0, 3);
+        const rest = sorted.slice(3).filter((m) => m.relevanceScore >= cfg.minRelevance);
+        filtered = [...guaranteed, ...rest].slice(0, limit);
+    }
+    else {
+        filtered = sorted.filter((m) => m.relevanceScore >= cfg.minRelevance).slice(0, limit);
+    }
+    const elapsed = performance.now() - startTime;
+    return {
+        memories: filtered,
+        totalActive,
+        totalArchived,
+        recallTimeMs: Math.round(elapsed * 100) / 100,
+        aggressive: cfg.aggressive,
+    };
+}
+/**
+ * Format recall results as a host-friendly <gnosys-recall> block.
+ * This is what gets injected into the model context on every turn
+ * via the MCP Resource. Citation-heavy with [[wikilinks]].
+ */
+export function formatRecall(result) {
+    if (result.memories.length === 0) {
+        return `<gnosys: no-strong-recall-needed>`;
+    }
+    const lines = [`<gnosys-recall>`];
+    for (let i = 0; i < result.memories.length; i++) {
+        const m = result.memories[i];
+        const archive = m.fromArchive ? " [ARCHIVED]" : "";
+        const filename = m.path.split("/").pop() || m.path;
+        lines.push(`[Memory ${i + 1}] [[${filename}]] (relevance: ${m.relevanceScore.toFixed(2)})${archive}`);
+        if (m.snippet) {
+            lines.push(m.snippet.substring(0, 250).replace(/\n/g, " ").trim());
+        }
+        lines.push("");
+    }
+    lines.push(`</gnosys-recall>`);
+    return lines.join("\n");
+}
+/**
+ * Format recall results as a concise CLI-friendly output.
+ */
+export function formatRecallCLI(result) {
+    const mode = result.aggressive ? "aggressive" : "filtered";
+    if (result.memories.length === 0) {
+        return `[Gnosys Recall] No relevant memories found. (${mode}, ${result.recallTimeMs}ms)`;
+    }
+    const lines = [
+        `[Gnosys Recall] ${result.memories.length} memories (${mode}, ${result.recallTimeMs}ms)`,
+        "",
+    ];
+    for (const m of result.memories) {
+        const archive = m.fromArchive ? " [ARCHIVED]" : "";
+        const score = m.relevanceScore.toFixed(2);
+        lines.push(`• ${m.title}${archive} (relevance: ${score})`);
+        lines.push(`  Category: ${m.category} | Confidence: ${m.confidence}`);
+        lines.push(`  Path: [[${m.path}]]`);
+        if (m.snippet) {
+            lines.push(`  ${m.snippet.substring(0, 150).replace(/\n/g, " ").trim()}`);
+        }
+        lines.push("");
+    }
+    return lines.join("\n");
+}
+//# sourceMappingURL=recall.js.map

package/dist/lib/recall.js.map

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package/dist/lib/resolver.d.ts

@@ -0,0 +1,116 @@
+/**
+ * Gnosys Store Resolver — Discovers and manages layered stores.
+ *
+ * Four layers, resolved in specificity order:
+ *   Project  (auto-discovered from cwd, writable, default write target)
+ *   Optional (GNOSYS_STORES, read-only)
+ *   Personal (GNOSYS_PERSONAL, writable, fallback write target)
+ *   Global   (GNOSYS_GLOBAL, writable only when explicitly targeted)
+ */
+import { GnosysStore, Memory } from "./store.js";
+export type StoreLayer = "project" | "personal" | "global" | "optional";
+export interface ResolvedStore {
+    layer: StoreLayer;
+    label: string;
+    store: GnosysStore;
+    writable: boolean;
+    path: string;
+}
+export interface LayeredMemory extends Memory {
+    sourceLayer: StoreLayer;
+    sourceLabel: string;
+}
+export declare class GnosysResolver {
+    private stores;
+    /** MCP workspace roots (file:// URIs → local paths). Updated via roots/list. */
+    private static mcpRoots;
+    /**
+     * Update the MCP roots list. Call this from the MCP server on init
+     * and on "notifications/roots/list_changed".
+     */
+    static setMcpRoots(roots: Array<{
+        uri: string;
+        name?: string;
+    }>): void;
+    /**
+     * Get the current MCP roots as local paths.
+     */
+    static getMcpRoots(): string[];
+    /**
+     * Create a resolver scoped to a specific project root.
+     * Used for per-tool projectRoot parameter — each call gets its own
+     * resolver instance, so there's no shared mutable state.
+     */
+    static resolveForProject(projectRoot: string): Promise<GnosysResolver>;
+    /**
+     * Discover and initialize all store layers.
+     */
+    resolve(): Promise<ResolvedStore[]>;
+    /**
+     * Get all stores in precedence order.
+     */
+    getStores(): ResolvedStore[];
+    /**
+     * Get all memories across all stores, tagged with their source.
+     */
+    getAllMemories(): Promise<LayeredMemory[]>;
+    /**
+     * Read a memory, searching stores in precedence order.
+     * Path format: "layer:category/filename.md" or just "category/filename.md" (searches all).
+     */
+    readMemory(memPath: string): Promise<LayeredMemory | null>;
+    /**
+     * Get the writable store for a given target layer.
+     *
+     * When no target is specified, auto-selects: project → personal.
+     * Global is writable but NEVER auto-selected — it must be explicitly
+     * requested (store: "global"). This prevents accidental writes to
+     * shared org knowledge.
+     * Optional stores are always read-only.
+     */
+    getWriteTarget(target?: StoreLayer): ResolvedStore | null;
+    /**
+     * Get a summary of all active stores for logging.
+     */
+    getSummary(): string;
+    /**
+     * Register a project directory in the persistent project registry.
+     * Called by gnosys_init after creating a new store.
+     */
+    registerProject(projectDir: string): Promise<void>;
+    /**
+     * Directly add a project store to the active stores list.
+     * Used after gnosys_init creates a store, to avoid re-resolving from cwd.
+     */
+    addProjectStore(storePath: string): Promise<void>;
+    /**
+     * Find a project store. Priority order:
+     *   1. Registered projects (~/.config/gnosys/projects.json)
+     *   2. MCP workspace roots (from roots/list)
+     *   3. Walk up from cwd (legacy fallback)
+     */
+    private findProjectStore;
+    /**
+     * Read registered project directories from persistent config.
+     */
+    private getRegisteredProjects;
+    /**
+     * Path to the persistent project registry file.
+     */
+    private getRegistryPath;
+    /**
+     * Detect all available stores from all sources (registered, MCP roots, cwd, env vars).
+     * Returns a flat list for debugging. Does NOT modify the active stores.
+     */
+    detectAllStores(): Promise<Array<{
+        source: string;
+        path: string;
+        hasGnosys: boolean;
+        isActive: boolean;
+    }>>;
+    /**
+     * Check if a path looks like a valid Gnosys store.
+     */
+    private isValidStore;
+}
+//# sourceMappingURL=resolver.d.ts.map

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

@@ -0,0 +1 @@
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