nodedex 0.1.0

package/dist/routes/flags.js

@@ -0,0 +1,151 @@
+// routes/flags.ts — pipeline_flags inspection + manual review override.
+//
+// DEBT 5 Slice 2 Sub-step 2.4. Surfaces the pipeline_flags table (written by
+// Stage FLAG in Slice 1 + Stage AUDIT in Sub-step 2.3, consumed by the async
+// reviewer in Sub-step 2.2) so a human/agent can inspect the enrichment-cycle
+// queue without waiting for the async worker — AND manually override a verdict.
+//
+// Pattern reference: routes/quarantine.ts (read-only list/summary/:id). This
+// adds ONE write path: POST /api/flags/:id/review for manual operator override.
+//
+// Visibility contract (matches quarantine): flags do NOT leak into /api/blocks,
+// /api/tree, /api/search. These /api/flags/* routes ARE the explicit opt-in
+// inspection surface.
+//
+// Endpoints:
+//   GET  /api/flags                — list (filters: flag_type, origin_writer,
+//                                    reviewed=true|false, block_id, limit)
+//   GET  /api/flags/summary        — counts (total, unreviewed, by_type, by_writer)
+//   GET  /api/flags/:id            — single flag + both blocks embedded
+//   POST /api/flags/:id/review     — manual override { verdict, reason,
+//                                    execute?, winning_block_id? }
+import { Router } from "express";
+import { ensurePipelineFlagsTable, listFlags, getFlagById, getAgentPendingFlags, summarizePipelineFlags, } from "../middleware/reflect/pipeline-flags.js";
+import { loadBlockSnapshot } from "../middleware/reflect/flag-reviewer.js";
+import { applyFlagVerdict } from "../middleware/reflect/apply-flag-verdict.js";
+import { renderAgentFlag } from "../middleware/reflect/render-agent-flag.js";
+export function createFlagsRouter(db) {
+    const router = Router();
+    const raw = db["db"];
+    // Idempotent — guarantees reads succeed even on a DB that never wrote a flag
+    // (table comes back empty). CREATE IF NOT EXISTS, safe to call once here.
+    ensurePipelineFlagsTable(raw);
+    // ─── Summary (declare BEFORE /:id so "summary" isn't captured as an id) ─────
+    router.get("/api/flags/summary", (_req, res) => {
+        try {
+            res.json(summarizePipelineFlags(raw));
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── Agent-pending (owner-unknown flags routed to the agent) ─────────────────
+    // Owner-unknown flags the reviewer refused to guess (Part 3) surface here as
+    // PLAIN-ENGLISH questions. The agent resolves from context or asks the user, then
+    // applies via POST /api/flags/:id/review. Declared BEFORE /:id. The context hook
+    // injects these each turn (the uncertain_references pattern).
+    router.get("/api/flags/agent-pending", (req, res) => {
+        try {
+            let limit = 20;
+            if (typeof req.query.limit === "string") {
+                const n = parseInt(req.query.limit, 10);
+                if (Number.isFinite(n) && n > 0)
+                    limit = n;
+            }
+            const flags = getAgentPendingFlags(raw, { limit });
+            const rendered = flags.map(f => renderAgentFlag(raw, f)).filter(Boolean);
+            res.json({ count: rendered.length, flags: rendered });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── List (filtered) ────────────────────────────────────────────────────────
+    router.get("/api/flags", (req, res) => {
+        try {
+            const opts = {};
+            if (typeof req.query.flag_type === "string")
+                opts.flag_type = req.query.flag_type;
+            if (typeof req.query.origin_writer === "string")
+                opts.origin_writer = req.query.origin_writer;
+            if (typeof req.query.block_id === "string")
+                opts.block_id = req.query.block_id;
+            if (typeof req.query.reviewed === "string")
+                opts.reviewed = req.query.reviewed === "true";
+            if (typeof req.query.limit === "string") {
+                const n = parseInt(req.query.limit, 10);
+                if (Number.isFinite(n) && n > 0)
+                    opts.limit = n;
+            }
+            const flags = listFlags(raw, opts);
+            res.json({ count: flags.length, flags });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── Single entry (flag + both blocks embedded for context) ──────────────────
+    router.get("/api/flags/:id", (req, res) => {
+        try {
+            const flag = getFlagById(raw, req.params.id);
+            if (!flag)
+                return res.status(404).json({ error: `no flag ${req.params.id}` });
+            res.json({
+                flag,
+                block_a: loadBlockSnapshot(raw, flag.block_id_a),
+                block_b: flag.block_id_b ? loadBlockSnapshot(raw, flag.block_id_b) : null,
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── Manual review override ───────────────────────────────────────────────────
+    // Body: { verdict, reason, execute?, winning_block_id? }
+    //   execute=true + verdict='merge' → run executeMerge synchronously
+    //     (archive loser + wire supersedes). winning_block_id REQUIRED + must be
+    //     one of the flag's two blocks.
+    //   execute=false / omitted → write verdict only, no graph mutation.
+    // 404 if flag already reviewed (don't silently re-review; the operator must
+    // see the existing verdict first).
+    router.post("/api/flags/:id/review", (req, res) => {
+        try {
+            const flag = getFlagById(raw, req.params.id);
+            if (!flag)
+                return res.status(404).json({ error: `no flag ${req.params.id}` });
+            if (flag.reviewed_at) {
+                return res.status(409).json({
+                    error: `flag ${req.params.id} already reviewed`,
+                    existing_verdict: flag.review_verdict,
+                    reviewed_at: flag.reviewed_at,
+                });
+            }
+            const body = req.body ?? {};
+            const verdict = body.verdict;
+            const reason = typeof body.reason === "string" ? body.reason : "";
+            const execute = body.execute === true;
+            const winning_block_id = typeof body.winning_block_id === "string" ? body.winning_block_id : null;
+            // Shared mechanics with the NL accept-path (apply-flag-verdict.ts) — one
+            // validation + merge implementation, so the two surfaces can't diverge.
+            const result = applyFlagVerdict(db, flag, { verdict, reason, execute, winning_block_id });
+            if (!result.ok) {
+                // MERGE_FAILED is a server-side failure; everything else is a bad request.
+                const status = result.code === "MERGE_FAILED" ? 500 :
+                    result.code === "ALREADY_REVIEWED" ? 409 : 400;
+                return res.status(status).json({ error: result.message });
+            }
+            res.json({
+                ok: true,
+                flag_id: flag.id,
+                verdict,
+                action_taken: result.action_taken,
+                winning_block_id: result.winning_block_id,
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    return router;
+}
+//# sourceMappingURL=flags.js.map

package/dist/routes/flags.js.map

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package/dist/routes/inject.d.ts

@@ -0,0 +1,4 @@
+import { Router } from "express";
+import { WorkspaceDB } from "../store/database.js";
+export declare function createInjectRouter(db: WorkspaceDB, dataDir: string): Router;
+//# sourceMappingURL=inject.d.ts.map

package/dist/routes/inject.d.ts.map

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package/dist/routes/inject.js

@@ -0,0 +1,183 @@
+// routes/inject.ts — per-turn context injection for non-Claude-Code agents.
+// Returns compact context (goals, dead ends, constraints, relevant blocks)
+// that an agent framework can prepend to messages each turn.
+//
+// Used by:
+//   - /api/chat proxy (internally, before forwarding to LLM)
+//   - "Two-line mode" agents (direct HTTP call each turn)
+//   - Any agent framework that wants Nodedex context without hooks
+import { Router } from "express";
+import { existsSync, readFileSync } from "fs";
+import path from "path";
+// ─── Sticky.md parser ────────────────────────────────────────────────────────
+function parseStickyFile(dataDir) {
+    // Try common locations for sticky.md
+    const candidates = [
+        path.resolve(dataDir, "../../sticky.md"), // Nodedex/sticky.md
+        path.resolve(dataDir, "../../../sticky.md"), // project root sticky.md
+    ];
+    for (const p of candidates) {
+        if (existsSync(p)) {
+            try {
+                const text = readFileSync(p, "utf8");
+                const result = {};
+                for (const line of text.split("\n")) {
+                    const match = line.match(/^(VISION|MACRO|MICRO|TASK|LAST|NAV):\s*(.+)/);
+                    if (match)
+                        result[match[1].toLowerCase()] = match[2].trim();
+                }
+                return Object.keys(result).length > 0 ? result : null;
+            }
+            catch { /* skip */ }
+        }
+    }
+    return null;
+}
+export function createInjectRouter(db, dataDir) {
+    const router = Router();
+    // ─── GET /api/agent-inject ─────────────────────────────────────────────────
+    // Returns compact context for injection into an agent's prompt each turn.
+    //
+    // Query params:
+    //   project  — project label (required for scoped results)
+    //   agent_id — agent identifier (for session tracking)
+    //   format   — "text" (default) or "json"
+    router.get("/api/agent-inject", (req, res) => {
+        try {
+            const project = req.query.project || "";
+            const agentId = req.query.agent_id || undefined;
+            const format = req.query.format || "text";
+            if (agentId)
+                db.registerAgent(agentId);
+            const allBlocks = db.getAllBlocks();
+            // ── Goals from sticky.md ────────────────────────────────────────
+            const goals = parseStickyFile(dataDir);
+            // ── Dead ends for this project ──────────────────────────────────
+            const deadEnds = project
+                ? allBlocks.filter(b => b.type === "dead_end" &&
+                    b.status !== "archived" &&
+                    b.label.startsWith(project + "_")).map(b => ({
+                    label: b.label,
+                    essence: (b.essence || "").slice(0, 120),
+                    unique: (() => {
+                        try {
+                            const c = typeof b.content === "string" ? JSON.parse(b.content) : b.content;
+                            return c?.unique ?? {};
+                        }
+                        catch {
+                            return {};
+                        }
+                    })(),
+                }))
+                : [];
+            // ── Constraints for this project ────────────────────────────────
+            const constraints = project
+                ? allBlocks.filter(b => b.type === "constraint" &&
+                    b.status !== "archived" &&
+                    b.label.startsWith(project + "_")).map(b => ({
+                    label: b.label,
+                    essence: (b.essence || "").slice(0, 120),
+                }))
+                : [];
+            // ── Open tasks ──────────────────────────────────────────────────
+            const openTasks = allBlocks.filter(b => {
+                if (b.type !== "task" || b.status === "archived")
+                    return false;
+                if (project && !b.label.startsWith(project + "_"))
+                    return false;
+                try {
+                    const c = JSON.parse(b.content);
+                    return c?.unique?.status !== "done";
+                }
+                catch {
+                    return true;
+                }
+            }).map(b => ({
+                label: b.label,
+                essence: (b.essence || "").slice(0, 100),
+            }));
+            // ── Collect block IDs for pipeline reflectedIds tracking ────────
+            const blockIds = [];
+            for (const de of deadEnds) {
+                const b = allBlocks.find(bl => bl.label === de.label);
+                if (b)
+                    blockIds.push(b.id);
+            }
+            for (const c of constraints) {
+                const b = allBlocks.find(bl => bl.label === c.label);
+                if (b)
+                    blockIds.push(b.id);
+            }
+            for (const t of openTasks) {
+                const b = allBlocks.find(bl => bl.label === t.label);
+                if (b)
+                    blockIds.push(b.id);
+            }
+            // ── Format response ─────────────────────────────────────────────
+            if (format === "json") {
+                return res.json({
+                    goals,
+                    dead_ends: deadEnds,
+                    constraints,
+                    open_tasks: openTasks,
+                    block_ids: [...new Set(blockIds)],
+                    project: project || null,
+                });
+            }
+            // Default: compact text format for direct injection
+            const lines = [];
+            if (goals) {
+                lines.push("═══ GOALS ═══");
+                if (goals.vision)
+                    lines.push(`VISION: ${goals.vision}`);
+                if (goals.macro)
+                    lines.push(`MACRO:  ${goals.macro}`);
+                if (goals.micro)
+                    lines.push(`MICRO:  ${goals.micro}`);
+                if (goals.task)
+                    lines.push(`TASK:   ${goals.task}`);
+                lines.push("");
+            }
+            if (deadEnds.length > 0) {
+                lines.push("═══ DEAD ENDS (do NOT re-propose these) ═══");
+                for (const de of deadEnds) {
+                    const reason = de.unique?.reason ? ` — ${de.unique.reason}` : "";
+                    lines.push(`  ${de.label}: ${de.essence}${reason}`);
+                }
+                lines.push("");
+            }
+            if (constraints.length > 0) {
+                lines.push("═══ CONSTRAINTS (cannot be overridden) ═══");
+                for (const c of constraints) {
+                    lines.push(`  ${c.label}: ${c.essence}`);
+                }
+                lines.push("");
+            }
+            if (openTasks.length > 0) {
+                lines.push("═══ OPEN TASKS ═══");
+                for (const t of openTasks) {
+                    lines.push(`  ${t.label}: ${t.essence}`);
+                }
+                lines.push("");
+            }
+            // Reminders — critical rules that agents forget
+            lines.push("═══ REMINDERS ═══");
+            lines.push("• Check dead ends before proposing any approach");
+            lines.push("• Reason in natural language — the pipeline extracts decisions, dead ends, and chains automatically");
+            lines.push("• Traverse the graph — search is the entry point, not the answer");
+            lines.push("• Does your current task trace back to VISION? If not, flag it.");
+            const text = lines.join("\n");
+            res.json({
+                context: text,
+                block_ids: [...new Set(blockIds)],
+                project: project || null,
+                char_count: text.length,
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    return router;
+}
+//# sourceMappingURL=inject.js.map

package/dist/routes/inject.js.map

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package/dist/routes/mcp-http.d.ts

@@ -0,0 +1,5 @@
+import { Router } from "express";
+import { WorkspaceDB } from "../store/database.js";
+import { EmbeddingEngine } from "../engine/embeddings.js";
+export declare function createMcpHttpRouter(db: WorkspaceDB, embeddings: EmbeddingEngine): Router;
+//# sourceMappingURL=mcp-http.d.ts.map

package/dist/routes/mcp-http.d.ts.map

@@ -0,0 +1 @@
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package/dist/routes/mcp-http.js

@@ -0,0 +1,94 @@
+// routes/mcp-http.ts — Streamable-HTTP MCP transport.
+//
+// WHY: the stdio transport (server.ts) only works when the MCP CLIENT can spawn the
+// server binary IN ITS OWN ENVIRONMENT. A containerized host (e.g. Hermes in Docker)
+// can't spawn a binary that lives on the Windows host — so it needs to reach the running
+// server over the NETWORK. This exposes the SAME tool surface (buildWorkspaceServer) over
+// HTTP at POST/GET/DELETE /mcp, so a client connects to e.g. http://host.docker.internal:3001/mcp.
+//
+// Stateful sessions: a client `initialize` mints a session (mcp-session-id header); later
+// requests reuse it. One McpServer per session (cheap), sharing the db/embeddings singletons.
+//
+// SECURITY: /mcp is NOT under /api, and the global requireAuth gate EXEMPTS non-/api paths
+// (defaultAuthExempt). Since /mcp is the WHOLE tool surface over the network, we gate it
+// HERE with the same owner token — otherwise binding 0.0.0.0 would expose it unauthenticated.
+import { Router } from "express";
+import { randomUUID } from "node:crypto";
+import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
+import { isInitializeRequest } from "@modelcontextprotocol/sdk/types.js";
+import { buildWorkspaceServer } from "../mcp-server.js";
+import { apiTokenEnabled, validateCredential, extractCredential, isLoopbackRequest } from "../middleware/auth.js";
+export function createMcpHttpRouter(db, embeddings) {
+    const router = Router();
+    // sessionId → transport. Cleaned up on transport close.
+    const transports = {};
+    // Same owner-token check as the rest of the API (the global gate exempts non-/api paths).
+    const authed = (req, res) => {
+        if (!apiTokenEnabled())
+            return true; // open when no token configured (localhost default)
+        if (isLoopbackRequest(req))
+            return true; // own machine — the token gates the network
+        if (validateCredential(extractCredential(req)))
+            return true;
+        res.status(401).json({
+            jsonrpc: "2.0",
+            error: { code: -32001, message: "Unauthorized — send 'x-nodedex-token' or 'Authorization: Bearer <token>' (NODEDEX_API_TOKEN is enabled)" },
+            id: null,
+        });
+        return false;
+    };
+    router.post("/mcp", async (req, res) => {
+        if (!authed(req, res))
+            return;
+        try {
+            const sid = req.headers["mcp-session-id"];
+            let transport;
+            if (sid && transports[sid]) {
+                transport = transports[sid]; // existing session
+            }
+            else if (!sid && isInitializeRequest(req.body)) {
+                // New session: mint a transport + a fresh server with the full tool surface.
+                transport = new StreamableHTTPServerTransport({
+                    sessionIdGenerator: () => randomUUID(),
+                    onsessioninitialized: (newId) => { transports[newId] = transport; },
+                });
+                transport.onclose = () => { if (transport.sessionId)
+                    delete transports[transport.sessionId]; };
+                const server = buildWorkspaceServer(db, embeddings);
+                await server.connect(transport);
+            }
+            else {
+                res.status(400).json({
+                    jsonrpc: "2.0",
+                    error: { code: -32000, message: "Bad Request: no valid session ID (call initialize first)" },
+                    id: null,
+                });
+                return;
+            }
+            // Cast: the SDK augments `req.auth` as AuthInfo, our auth.ts augments it as
+            // AuthIdentity — two module augmentations of the same global clash at the type
+            // level only. The runtime objects are plain Express req/res, which the SDK accepts.
+            await transport.handleRequest(req, res, req.body);
+        }
+        catch (e) {
+            if (!res.headersSent) {
+                res.status(500).json({ jsonrpc: "2.0", error: { code: -32603, message: String(e) }, id: null });
+            }
+        }
+    });
+    // GET = open the SSE stream; DELETE = terminate the session. Both need an existing session.
+    const bySession = async (req, res) => {
+        if (!authed(req, res))
+            return;
+        const sid = req.headers["mcp-session-id"];
+        if (!sid || !transports[sid]) {
+            res.status(400).send("Invalid or missing mcp-session-id");
+            return;
+        }
+        await transports[sid].handleRequest(req, res);
+    };
+    router.get("/mcp", bySession);
+    router.delete("/mcp", bySession);
+    return router;
+}
+//# sourceMappingURL=mcp-http.js.map

package/dist/routes/mcp-http.js.map

@@ -0,0 +1 @@
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package/dist/routes/quarantine.d.ts

@@ -0,0 +1,4 @@
+import { Router } from "express";
+import { WorkspaceDB } from "../store/database.js";
+export declare function createQuarantineRouter(db: WorkspaceDB): Router;
+//# sourceMappingURL=quarantine.d.ts.map

package/dist/routes/quarantine.d.ts.map

@@ -0,0 +1 @@
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package/dist/routes/quarantine.js

@@ -0,0 +1,66 @@
+// routes/quarantine.ts — READ-ONLY observability for the Pass-2-split audit quarantine.
+//
+// Purpose (debt-2 step 4, 2026-05-26): surface the `pass2_audit_quarantine` table
+// so we can gather REAL data on what accumulates there before designing the full
+// enrichment cycle (§§4-9 of DEBT2-ENRICHMENT-DESIGN.md). The reader API already
+// exists in middleware/reflect/pass2-quarantine.ts; this just wires it to HTTP.
+//
+// SCOPE: read-only. No promote, no clarify, no writes. Those are the enrichment
+// surface and wait on the §§4-9 design + empirical evidence this endpoint gathers.
+//
+// Visibility contract (PASS2-SPLIT-DESIGN §3): quarantine is an explicit opt-in
+// surface, NEVER part of default agent navigation. These /api/quarantine/* routes
+// ARE that explicit opt-in — they don't leak into /api/blocks, /api/tree, search.
+import { Router } from "express";
+import { ensureQuarantineTable, getQuarantineEntry, getQuarantineEntries, summarizeQuarantine, } from "../middleware/reflect/pass2-quarantine.js";
+export function createQuarantineRouter(db) {
+    const router = Router();
+    const raw = db["db"];
+    // Idempotent: guarantees reads succeed even on a DB that never ran split-mode
+    // (the table just comes back empty). CREATE IF NOT EXISTS — safe to call once here.
+    ensureQuarantineTable(raw);
+    // ─── Summary (tier-signal primitive) ──────────────────────────────────────
+    // MUST be declared before /:id so "summary" isn't captured as an id.
+    router.get("/api/quarantine/summary", (_req, res) => {
+        try {
+            res.json(summarizeQuarantine(raw));
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── List (filtered) ───────────────────────────────────────────────────────
+    router.get("/api/quarantine", (req, res) => {
+        try {
+            const filters = {};
+            if (typeof req.query.batch_id === "string")
+                filters.batch_id = req.query.batch_id;
+            if (typeof req.query.source_session_id === "string")
+                filters.source_session_id = req.query.source_session_id;
+            if (typeof req.query.failure_reason === "string")
+                filters.failure_reason = req.query.failure_reason;
+            if (typeof req.query.queued_for_enrichment === "string") {
+                filters.queued_for_enrichment = req.query.queued_for_enrichment === "true";
+            }
+            const entries = getQuarantineEntries(raw, filters);
+            res.json({ count: entries.length, entries });
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    // ─── Single entry (full audit trail) ──────────────────────────────────────
+    router.get("/api/quarantine/:id", (req, res) => {
+        try {
+            const entry = getQuarantineEntry(raw, req.params.id);
+            if (!entry)
+                return res.status(404).json({ error: `no quarantine entry ${req.params.id}` });
+            res.json(entry);
+        }
+        catch (e) {
+            res.status(500).json({ error: String(e) });
+        }
+    });
+    return router;
+}
+//# sourceMappingURL=quarantine.js.map

package/dist/routes/quarantine.js.map

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package/dist/routes/recall.d.ts

@@ -0,0 +1,5 @@
+import { Router } from "express";
+import { WorkspaceDB } from "../store/database.js";
+import { EmbeddingEngine } from "../engine/embeddings.js";
+export declare function createRecallRouter(db: WorkspaceDB, embeddings?: EmbeddingEngine): Router;
+//# sourceMappingURL=recall.d.ts.map

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

@@ -0,0 +1 @@
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