gnosys 5.5.0 → 5.7.0

package/dist/lib/chat/write.js

@@ -0,0 +1,203 @@
+/**
+ * Chat-side memory writing — promote chat content to gnosys memories.
+ *
+ * Handles three triggers:
+ *   /remember <text>     explicit user-marked insight
+ *   /save-turn           distill the last user+assistant exchange
+ *   /attach <file>       ingest a file via the multimodal pipeline
+ *
+ * All promoted memories carry session provenance:
+ *   tags.session: [<sessionId>]
+ *   tags.from-chat: ["true"]
+ *   tags.source: ["remember" | "save-turn" | "auto" | "attach"]
+ */
+import { getLLMProvider } from "../llm.js";
+/** Build the structuring prompt for save-turn / auto-promote (LLM-assisted). */
+function buildStructurePrompt(content, source) {
+    return `You are extracting one memory from chat content. Output STRICT JSON only — no markdown fences, no commentary.
+
+Schema:
+{
+  "title": "<5–10 word title>",
+  "category": "decisions | architecture | concepts | requirements | landscape | open-questions | roadmap",
+  "tags": ["<3–6 lowercase domain words>"],
+  "relevance": "<space-separated keyword cloud for discovery>"
+}
+
+Source: ${source}
+Content:
+${content}
+
+Output the JSON object only.`;
+}
+const VALID_CATEGORIES = new Set([
+    "decisions",
+    "architecture",
+    "concepts",
+    "requirements",
+    "landscape",
+    "open-questions",
+    "roadmap",
+]);
+const FALLBACK_CATEGORY = {
+    remember: "concepts",
+    "save-turn": "concepts",
+    auto: "decisions",
+    attach: "concepts",
+};
+/** Heuristic fallback when LLM isn't available. Uses the first line as the title. */
+function deriveFieldsFallback(content, source) {
+    const firstLine = content.split(/\n/, 1)[0].trim();
+    const title = firstLine.length > 60 ? firstLine.slice(0, 57) + "..." : firstLine || "Memory";
+    return {
+        title,
+        category: FALLBACK_CATEGORY[source],
+        tags: [],
+        relevance: content.split(/\s+/).slice(0, 20).join(" "),
+    };
+}
+async function deriveFieldsViaLLM(config, content, source) {
+    try {
+        const provider = getLLMProvider(config, "structuring");
+        const raw = await provider.generate(buildStructurePrompt(content, source), { maxTokens: 400 });
+        // Tolerate the model returning ```json ... ``` despite our instructions
+        const trimmed = raw.replace(/^```(?:json)?\s*|\s*```$/g, "").trim();
+        const parsed = JSON.parse(trimmed);
+        if (!parsed.title || !parsed.category)
+            return null;
+        return {
+            title: parsed.title,
+            category: VALID_CATEGORIES.has(parsed.category) ? parsed.category : FALLBACK_CATEGORY[source],
+            tags: Array.isArray(parsed.tags) ? parsed.tags.map(String) : [],
+            relevance: typeof parsed.relevance === "string" ? parsed.relevance : "",
+        };
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Write a chat-sourced memory to the central DB. Returns the assigned ID.
+ *
+ * Uses LLM structuring when config is provided and the structuring provider
+ * is reachable; falls back to a heuristic title + category otherwise.
+ */
+export async function promoteToMemory(db, opts) {
+    // Try LLM first; fall back if unavailable or on error
+    let fields = null;
+    if (opts.config) {
+        fields = await deriveFieldsViaLLM(opts.config, opts.content, opts.source);
+    }
+    if (!fields) {
+        fields = deriveFieldsFallback(opts.content, opts.source);
+    }
+    // Caller-provided overrides win
+    if (opts.title)
+        fields.title = opts.title;
+    if (opts.category && VALID_CATEGORIES.has(opts.category))
+        fields.category = opts.category;
+    // Provenance tags injected on top of any LLM-suggested ones
+    const allTags = [
+        ...fields.tags,
+        `session:${opts.sessionId}`,
+        `from-chat:true`,
+        `source:${opts.source}`,
+    ];
+    const id = db.getNextId(fields.category, opts.projectId ?? undefined);
+    const now = new Date().toISOString();
+    const today = now.split("T")[0];
+    const memory = {
+        id,
+        title: fields.title,
+        category: fields.category,
+        content: `# ${fields.title}\n\n${opts.content}`,
+        summary: null,
+        tags: JSON.stringify(allTags),
+        relevance: fields.relevance,
+        author: opts.source === "auto" ? "ai" : "human+ai",
+        authority: "declared",
+        confidence: 0.85,
+        reinforcement_count: 0,
+        content_hash: fnv1a(opts.content),
+        status: "active",
+        tier: "active",
+        supersedes: null,
+        superseded_by: null,
+        last_reinforced: null,
+        created: today,
+        modified: today,
+        source_path: null,
+        project_id: opts.projectId,
+        scope: opts.projectId ? "project" : "user",
+    };
+    db.insertMemory(memory);
+    db.logAudit({
+        timestamp: now,
+        operation: "write",
+        memory_id: id,
+        details: JSON.stringify({ source: `chat:${opts.source}`, sessionId: opts.sessionId }),
+        duration_ms: null,
+        trace_id: null,
+    });
+    return { id, title: fields.title, category: fields.category };
+}
+/** Build the content for /save-turn from the most recent user+assistant exchange. */
+export function lastExchange(buffer) {
+    // Walk from the end to find the last assistant turn, then the user turn before it
+    let assistantIdx = -1;
+    for (let i = buffer.length - 1; i >= 0; i--) {
+        if (buffer[i].role === "assistant") {
+            assistantIdx = i;
+            break;
+        }
+    }
+    if (assistantIdx < 1)
+        return null;
+    let userIdx = -1;
+    for (let i = assistantIdx - 1; i >= 0; i--) {
+        if (buffer[i].role === "user") {
+            userIdx = i;
+            break;
+        }
+    }
+    if (userIdx < 0)
+        return null;
+    return {
+        user: buffer[userIdx].text,
+        assistant: buffer[assistantIdx].text,
+    };
+}
+/** Format a save-turn pair as a markdown exchange suitable for memory content. */
+export function formatExchange(pair) {
+    return `**Question / context:**\n${pair.user}\n\n**Answer / decision:**\n${pair.assistant}`;
+}
+// ─── Auto-promote heuristic ──────────────────────────────────────────────
+const AUTO_PROMOTE_PATTERNS = [
+    { pattern: /\b(we (decided|agreed|chose) to|let's (go with|commit to|use))\b/i, source: "auto", reason: "decision-language" },
+    { pattern: /\b(I learned|the answer is|turns out|it works because)\b/i, source: "auto", reason: "insight-language" },
+    { pattern: /\b(let's note|note that|let's remember|don't forget)\b/i, source: "auto", reason: "note-request" },
+];
+/**
+ * Scan a user turn for "looks like a decision/insight worth saving" patterns.
+ * Returns a hint that the TUI can surface as an inline confirm prompt.
+ * Returns null when nothing matches.
+ */
+export function detectAutoPromote(userText) {
+    for (const { pattern, reason } of AUTO_PROMOTE_PATTERNS) {
+        const m = userText.match(pattern);
+        if (m) {
+            return { reason, match: m[0] };
+        }
+    }
+    return null;
+}
+// ─── helpers ─────────────────────────────────────────────────────────────
+function fnv1a(text) {
+    let hash = 0x811c9dc5;
+    for (let i = 0; i < text.length; i++) {
+        hash ^= text.charCodeAt(i);
+        hash = Math.imul(hash, 0x01000193);
+    }
+    return (hash >>> 0).toString(16).padStart(8, "0");
+}
+//# sourceMappingURL=write.js.map

package/dist/lib/chat/write.js.map

@@ -0,0 +1 @@
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package/dist/lib/db.d.ts

@@ -145,6 +145,23 @@ export declare class GnosysDB {
      * file handles after a WAL checkpoint or remount.
      */
     reopen(): void;
+    /**
+     * Execute a DB operation with automatic recovery from stale-handle errors.
+     *
+     * SQLITE_CORRUPT ("database disk image is malformed") can happen when a
+     * long-lived handle (e.g. an MCP server process) sees stale pages after
+     * concurrent writes from another process (`gnosys setup`, sync layer, etc.)
+     * truncated the WAL or rolled the schema. The DB file itself is fine —
+     * just our cached page view is out of date.
+     *
+     * Strategy: catch the error, close + reopen the handle, retry once. If it
+     * still fails after reopen, rethrow — that's a real corruption case.
+     *
+     * Used internally by write methods that the MCP server calls long-term.
+     * Read methods are also wrapped because reads against stale pages can
+     * surface the same error.
+     */
+    private withRecovery;
     /**
      * Restore from a backup file. Closes current DB, copies backup over, re-opens.
      */
@@ -169,6 +186,8 @@ export declare class GnosysDB {
     getAllMemories(): DbMemory[];
     getMemoriesByTier(tier: string): DbMemory[];
     getMemoriesByCategory(category: string): DbMemory[];
+    getRelationshipsForMemoryIds(ids: string[]): DbRelationship[];
+    getAuditEntriesByProject(projectId: string): DbAuditEntry[];
     updateMemory(id: string, updates: Partial<DbMemory>): void;
     deleteMemory(id: string): void;
     getMemoryCount(): {
@@ -180,7 +199,7 @@ export declare class GnosysDB {
     /**
      * Get active memories scoped to a specific project.
      */
-    getMemoriesByProject(projectId: string): DbMemory[];
+    getMemoriesByProject(projectId: string, includeArchived?: boolean): DbMemory[];
     /**
      * Get memories by scope (project, user, global).
      */
@@ -232,6 +251,27 @@ export declare class GnosysDB {
     getAllSummaries(): DbSummary[];
     logAudit(entry: Omit<DbAuditEntry, "id">): void;
     getAuditLog(memoryId: string, limit?: number): DbAuditEntry[];
+    /**
+     * Get audit entries newer than a given timestamp. Used by remote sync to
+     * push/pull audit_log incrementally. Returns oldest-first so order is
+     * preserved across machines.
+     */
+    getAuditEntriesAfter(sinceIso: string, limit?: number): DbAuditEntry[];
+    /**
+     * Get the most recent audit timestamp seen in this DB. Used as a high-water
+     * mark for sync: "push entries newer than the most recent timestamp the
+     * remote has already seen". Returns null when the table is empty.
+     */
+    getLatestAuditTimestamp(): string | null;
+    /**
+     * Query audit entries with optional filters. Returns newest first.
+     * Used by `gnosys audit` and `gnosys doctor` reports.
+     */
+    queryAuditLog(opts?: {
+        sinceIso?: string;
+        operation?: string;
+        limit?: number;
+    }): DbAuditEntry[];
     updateEmbedding(id: string, embedding: Buffer): void;
     getEmbedding(id: string): Buffer | null;
     getAllEmbeddings(): Array<{

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

@@ -1 +1 @@
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+{"version":3,"file":"db.d.ts","sourceRoot":"","sources":["../../src/lib/db.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAmBH,MAAM,WAAW,QAAQ;IACvB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAE3B,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAEhC,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,kDAAkD;AAClD,MAAM,WAAW,SAAS;IACxB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,iBAAiB,EAAE,MAAM,CAAC;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,kBAAkB,EAAE,MAAM,GAAG,IAAI,CAAC;IAClC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,MAAM,WAAW,GAAG,SAAS,GAAG,MAAM,GAAG,QAAQ,CAAC;AAExD,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,SAAS;IACxB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;CACzB;AAED,MAAM,WAAW,cAAc;IAC7B,gBAAgB,EAAE,MAAM,CAAC;IACzB,eAAe,EAAE,MAAM,CAAC;IACxB,oBAAoB,EAAE,MAAM,CAAC;IAC7B,QAAQ,EAAE,OAAO,CAAC;CACnB;AAgLD,iBAAS,KAAK,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAOlC;AAID,qBAAa,QAAQ;IAEnB,OAAO,CAAC,EAAE,CAAa;IACvB,OAAO,CAAC,SAAS,CAAS;IAC1B,OAAO,CAAC,SAAS,CAAS;IAC1B,OAAO,CAAC,UAAU,CAAS;IAE3B;;;;OAIG;IACH,MAAM,CAAC,aAAa,IAAI,MAAM;IAI9B,8EAA8E;IAC9E,MAAM,CAAC,eAAe,IAAI,MAAM;IAIhC;;OAEG;IACH,MAAM,CAAC,gBAAgB,IAAI,MAAM;IAIjC;;;;;;;;;;;;;;OAcG;IACH,MAAM,CAAC,WAAW,IAAI,QAAQ;IAoD9B;;;OAGG;IACH,MAAM,CAAC,SAAS,IAAI,QAAQ;gBAMhB,SAAS,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE;QAAE,OAAO,CAAC,EAAE,MAAM,CAAC;QAAC,YAAY,CAAC,EAAE,MAAM,CAAA;KAAE;IAgCjF;;;OAGG;IACG,MAAM,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAUjD;;;;;;OAMG;IACH,MAAM,CAAC,iBAAiB,CAAC,GAAG,EAAE,OAAO,GAAG,OAAO;IAY/C;;;OAGG;IACH,MAAM,CAAC,8BAA8B,IAAI,MAAM;IAmB/C;;;OAGG;IACH,MAAM,IAAI,IAAI;IAoBd;;;;;;;;;;;;;;;OAeG;IACH,OAAO,CAAC,YAAY;IAwBpB;;OAEG;IACH,MAAM,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,GAAG,QAAQ;IAgBhE,OAAO,CAAC,WAAW;IAkBnB;;;OAGG;IACH,OAAO,CAAC,aAAa;IA+DrB,WAAW,IAAI,OAAO;IAItB,SAAS,IAAI,MAAM;IAInB,YAAY,IAAI,MAAM;IAMtB,YAAY,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,EAAE,WAAW,GAAG,aAAa,GAAG,aAAa,GAAG,kBAAkB,CAAC,GAAG;QAAE,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,IAAI,CAAA;KAAE,GAAG,IAAI;IAyBrO,SAAS,CAAC,EAAE,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI;IAMtC,iBAAiB,IAAI,QAAQ,EAAE;IAM/B,cAAc,IAAI,QAAQ,EAAE;IAI5B,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ,EAAE;IAI3C,qBAAqB,CAAC,QAAQ,EAAE,MAAM,GAAG,QAAQ,EAAE;IAInD,4BAA4B,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,cAAc,EAAE;IAU7D,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,YAAY,EAAE;IAQ3D,YAAY,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,QAAQ,CAAC,GAAG,IAAI;IA0D1D,YAAY,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI;IA6B9B,cAAc,IAAI;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE;IAMrE,aAAa,IAAI,MAAM,EAAE;IAOzB;;OAEG;IACH,oBAAoB,CAAC,SAAS,EAAE,MAAM,EAAE,eAAe,UAAQ,GAAG,QAAQ,EAAE;IAO5E;;OAEG;IACH,kBAAkB,CAAC,KAAK,EAAE,WAAW,GAAG,QAAQ,EAAE;IAQlD,aAAa,CAAC,OAAO,EAAE,SAAS,GAAG,IAAI;IAcvC,UAAU,CAAC,EAAE,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAMxC,qBAAqB,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAMpD,cAAc,IAAI,SAAS,EAAE;IAM7B,aAAa,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,SAAS,CAAC,GAAG,IAAI;IAc5D,aAAa,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI;IAI/B;;;OAGG;IACH,gBAAgB,CAAC,aAAa,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM;IAOpE;;;;;;;;;;;;;;OAcG;IAEH,SAAS,CAAC,QAAQ,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM;IAOvD,SAAS,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,GAAE,MAAW,GAAG,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IAyBjH,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,GAAE,MAAW,GAAG,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IA8BrH,kBAAkB,CAAC,GAAG,EAAE,cAAc,GAAG,IAAI;IAO7C,oBAAoB,CAAC,EAAE,EAAE,MAAM,GAAG,cAAc,EAAE;IAIlD,kBAAkB,CAAC,EAAE,EAAE,MAAM,GAAG,cAAc,EAAE;IAMhD,aAAa,CAAC,OAAO,EAAE,SAAS,GAAG,IAAI;IAWvC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,SAA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package/dist/lib/db.js

@@ -400,6 +400,43 @@ export class GnosysDB {
             // reopen failed — leave unavailable; caller surfaces error
         }
     }
+    /**
+     * Execute a DB operation with automatic recovery from stale-handle errors.
+     *
+     * SQLITE_CORRUPT ("database disk image is malformed") can happen when a
+     * long-lived handle (e.g. an MCP server process) sees stale pages after
+     * concurrent writes from another process (`gnosys setup`, sync layer, etc.)
+     * truncated the WAL or rolled the schema. The DB file itself is fine —
+     * just our cached page view is out of date.
+     *
+     * Strategy: catch the error, close + reopen the handle, retry once. If it
+     * still fails after reopen, rethrow — that's a real corruption case.
+     *
+     * Used internally by write methods that the MCP server calls long-term.
+     * Read methods are also wrapped because reads against stale pages can
+     * surface the same error.
+     */
+    withRecovery(fn) {
+        try {
+            return fn();
+        }
+        catch (err) {
+            const errAny = err;
+            const isCorrupt = errAny?.code === "SQLITE_CORRUPT" ||
+                /database disk image is malformed/i.test(errAny?.message ?? "");
+            if (!isCorrupt)
+                throw err;
+            // One-shot recovery: reopen and retry. If the reopen itself fails or
+            // the retry surfaces the same error, that's a real corruption case —
+            // surface it loudly.
+            this.reopen();
+            if (!this.available) {
+                throw new Error("Gnosys DB unrecoverable after reopen. The underlying file may be corrupted. " +
+                    "Run 'gnosys doctor' for diagnostics; restore from a backup if needed.");
+            }
+            return fn();
+        }
+    }
     /**
      * Restore from a backup file. Closes current DB, copies backup over, re-opens.
      */
@@ -511,25 +548,27 @@ export class GnosysDB {
     }
     // ─── Memory CRUD ────────────────────────────────────────────────────
     insertMemory(mem) {
-        const stmt = this.db.prepare(`
-      INSERT OR REPLACE INTO memories
-        (id, title, category, content, summary, tags, relevance, author, authority,
-         confidence, reinforcement_count, content_hash, status, tier, supersedes,
-         superseded_by, last_reinforced, created, modified, embedding, source_path,
-         source_file, source_page, source_timerange,
-         project_id, scope)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-    `);
-        stmt.run(mem.id, mem.title, mem.category, mem.content, mem.summary || null, mem.tags, mem.relevance, mem.author, mem.authority, mem.confidence, mem.reinforcement_count, mem.content_hash, mem.status, mem.tier, mem.supersedes || null, mem.superseded_by || null, mem.last_reinforced || null, mem.created, mem.modified, mem.embedding || null, mem.source_path || null, mem.source_file || null, mem.source_page || null, mem.source_timerange || null, mem.project_id || null, mem.scope || "project");
+        return this.withRecovery(() => {
+            const stmt = this.db.prepare(`
+        INSERT OR REPLACE INTO memories
+          (id, title, category, content, summary, tags, relevance, author, authority,
+           confidence, reinforcement_count, content_hash, status, tier, supersedes,
+           superseded_by, last_reinforced, created, modified, embedding, source_path,
+           source_file, source_page, source_timerange,
+           project_id, scope)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+      `);
+            stmt.run(mem.id, mem.title, mem.category, mem.content, mem.summary || null, mem.tags, mem.relevance, mem.author, mem.authority, mem.confidence, mem.reinforcement_count, mem.content_hash, mem.status, mem.tier, mem.supersedes || null, mem.superseded_by || null, mem.last_reinforced || null, mem.created, mem.modified, mem.embedding || null, mem.source_path || null, mem.source_file || null, mem.source_page || null, mem.source_timerange || null, mem.project_id || null, mem.scope || "project");
+        });
     }
     getMemory(id) {
-        return this.db.prepare("SELECT * FROM memories WHERE id = ?").get(id) || null;
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM memories WHERE id = ?").get(id) || null);
     }
     getActiveMemories() {
-        return this.db.prepare("SELECT * FROM memories WHERE tier = 'active' AND status = 'active'").all();
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM memories WHERE tier = 'active' AND status = 'active'").all());
     }
     getAllMemories() {
-        return this.db.prepare("SELECT * FROM memories").all();
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM memories").all());
     }
     getMemoriesByTier(tier) {
         return this.db.prepare("SELECT * FROM memories WHERE tier = ?").all(tier);
@@ -537,6 +576,19 @@ export class GnosysDB {
     getMemoriesByCategory(category) {
         return this.db.prepare("SELECT * FROM memories WHERE category = ? AND tier = 'active'").all(category);
     }
+    getRelationshipsForMemoryIds(ids) {
+        if (ids.length === 0)
+            return [];
+        const placeholders = ids.map(() => "?").join(",");
+        return this.db
+            .prepare(`SELECT * FROM relationships WHERE source_id IN (${placeholders}) OR target_id IN (${placeholders})`)
+            .all(...ids, ...ids);
+    }
+    getAuditEntriesByProject(projectId) {
+        return this.db
+            .prepare("SELECT * FROM audit_log WHERE memory_id IN (SELECT id FROM memories WHERE project_id = ?) ORDER BY id")
+            .all(projectId);
+    }
     updateMemory(id, updates) {
         const fields = [];
         const values = [];
@@ -635,8 +687,11 @@ export class GnosysDB {
     /**
      * Get active memories scoped to a specific project.
      */
-    getMemoriesByProject(projectId) {
-        return this.db.prepare("SELECT * FROM memories WHERE project_id = ? AND tier = 'active' AND status = 'active'").all(projectId);
+    getMemoriesByProject(projectId, includeArchived = false) {
+        const sql = includeArchived
+            ? "SELECT * FROM memories WHERE project_id = ?"
+            : "SELECT * FROM memories WHERE project_id = ? AND tier = 'active' AND status = 'active'";
+        return this.db.prepare(sql).all(projectId);
     }
     /**
      * Get memories by scope (project, user, global).
@@ -646,20 +701,22 @@ export class GnosysDB {
     }
     // ─── Project Identity (v3.0) ──────────────────────────────────────
     insertProject(project) {
-        this.db.prepare(`
-      INSERT OR REPLACE INTO projects
-        (id, name, working_directory, user, agent_rules_target, obsidian_vault, created, modified)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?)
-    `).run(project.id, project.name, project.working_directory, project.user, project.agent_rules_target || null, project.obsidian_vault || null, project.created, project.modified);
+        return this.withRecovery(() => {
+            this.db.prepare(`
+        INSERT OR REPLACE INTO projects
+          (id, name, working_directory, user, agent_rules_target, obsidian_vault, created, modified)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+      `).run(project.id, project.name, project.working_directory, project.user, project.agent_rules_target || null, project.obsidian_vault || null, project.created, project.modified);
+        });
     }
     getProject(id) {
-        return this.db.prepare("SELECT * FROM projects WHERE id = ?").get(id) || null;
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM projects WHERE id = ?").get(id) || null);
     }
     getProjectByDirectory(dir) {
-        return this.db.prepare("SELECT * FROM projects WHERE working_directory = ?").get(dir) || null;
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM projects WHERE working_directory = ?").get(dir) || null);
     }
     getAllProjects() {
-        return this.db.prepare("SELECT * FROM projects ORDER BY name").all();
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM projects ORDER BY name").all());
     }
     updateProject(id, updates) {
         const fields = [];
@@ -797,13 +854,64 @@ export class GnosysDB {
     }
     // ─── Audit ──────────────────────────────────────────────────────────
     logAudit(entry) {
-        this.db.prepare(`
-      INSERT INTO audit_log (timestamp, operation, memory_id, details, duration_ms, trace_id)
-      VALUES (?, ?, ?, ?, ?, ?)
-    `).run(entry.timestamp, entry.operation, entry.memory_id, entry.details, entry.duration_ms, entry.trace_id);
+        return this.withRecovery(() => {
+            this.db.prepare(`
+        INSERT INTO audit_log (timestamp, operation, memory_id, details, duration_ms, trace_id)
+        VALUES (?, ?, ?, ?, ?, ?)
+      `).run(entry.timestamp, entry.operation, entry.memory_id, entry.details, entry.duration_ms, entry.trace_id);
+        });
     }
     getAuditLog(memoryId, limit = 20) {
-        return this.db.prepare("SELECT * FROM audit_log WHERE memory_id = ? ORDER BY timestamp DESC LIMIT ?").all(memoryId, limit);
+        return this.withRecovery(() => this.db.prepare("SELECT * FROM audit_log WHERE memory_id = ? ORDER BY timestamp DESC LIMIT ?").all(memoryId, limit));
+    }
+    /**
+     * Get audit entries newer than a given timestamp. Used by remote sync to
+     * push/pull audit_log incrementally. Returns oldest-first so order is
+     * preserved across machines.
+     */
+    getAuditEntriesAfter(sinceIso, limit) {
+        return this.withRecovery(() => {
+            const cap = limit ? ` LIMIT ${Math.max(1, Math.floor(limit))}` : "";
+            return this.db
+                .prepare(`SELECT * FROM audit_log WHERE timestamp > ? ORDER BY timestamp ASC${cap}`)
+                .all(sinceIso);
+        });
+    }
+    /**
+     * Get the most recent audit timestamp seen in this DB. Used as a high-water
+     * mark for sync: "push entries newer than the most recent timestamp the
+     * remote has already seen". Returns null when the table is empty.
+     */
+    getLatestAuditTimestamp() {
+        return this.withRecovery(() => {
+            const row = this.db
+                .prepare("SELECT timestamp FROM audit_log ORDER BY timestamp DESC LIMIT 1")
+                .get();
+            return row?.timestamp ?? null;
+        });
+    }
+    /**
+     * Query audit entries with optional filters. Returns newest first.
+     * Used by `gnosys audit` and `gnosys doctor` reports.
+     */
+    queryAuditLog(opts = {}) {
+        return this.withRecovery(() => {
+            const conditions = [];
+            const params = [];
+            if (opts.sinceIso) {
+                conditions.push("timestamp >= ?");
+                params.push(opts.sinceIso);
+            }
+            if (opts.operation) {
+                conditions.push("operation = ?");
+                params.push(opts.operation);
+            }
+            const where = conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "";
+            const limit = opts.limit ? ` LIMIT ${Math.max(1, Math.floor(opts.limit))}` : "";
+            return this.db
+                .prepare(`SELECT * FROM audit_log ${where} ORDER BY timestamp DESC${limit}`)
+                .all(...params);
+        });
     }
     // ─── Embeddings ─────────────────────────────────────────────────────
     updateEmbedding(id, embedding) {