@codified/cli 0.3.9 → 0.4.0

package/dist/commands/connect.js

@@ -105,9 +105,20 @@ async function verifyConnector(type, credentials) {
             };
             break;
         }
+        case "docs": {
+            authConfig.credentials = {
+                basePath: credentials.basePath ?? process.cwd(),
+            };
+            if (credentials.scanDirs) {
+                authConfig.credentials.scanDirs = Array.isArray(credentials.scanDirs)
+                    ? credentials.scanDirs.join(",")
+                    : String(credentials.scanDirs);
+            }
+            break;
+        }
     }
     // This calls the real API to authenticate
-    await ingest.registry.connect(type, authConfig);
+    await ingest.registry.connect(type === "docs" ? "markdown" : type, authConfig);
 }
 // ── Subcommand: slack ─────────────────────────────────────────────────
 const slackSubcommand = new Command("slack")
@@ -238,6 +249,42 @@ const notionSubcommand = new Command("notion")
         process.exit(1);
     }
 });
+// ── Subcommand: docs ──────────────────────────────────────────────────
+const docsSubcommand = new Command("docs")
+    .description("Connect local markdown documentation (docs/, adr/, decisions/)")
+    .argument("[path]", "Custom directory path to scan (default: docs/, adr/, decisions/)")
+    .action(async (customPath) => {
+    try {
+        console.log("\n  Codify Connect — Markdown Documents\n");
+        const basePath = process.cwd();
+        const credentials = {
+            basePath,
+        };
+        if (customPath) {
+            // Custom path: scan only the specified directory
+            credentials.scanDirs = [customPath];
+            console.log(`  Scanning: ${resolve(basePath, customPath)}`);
+        }
+        else {
+            console.log(`  Scanning default directories: docs/, adr/, decisions/`);
+        }
+        console.log(`  Verifying directories exist...`);
+        await verifyConnector("docs", credentials);
+        const entry = addConnector({
+            type: "docs",
+            credentials,
+        });
+        const scope = customPath ?? "docs/, adr/, decisions/";
+        console.log(`\n  Connected! ID: ${entry.id}`);
+        console.log(`  Directories: ${scope}`);
+        console.log(`\n  Run 'codify bootstrap' to mine documents into the context graph.\n`);
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        console.error(`\n  ERROR: ${message}\n`);
+        process.exit(1);
+    }
+});
 // ── Subcommand: list ──────────────────────────────────────────────────
 const listSubcommand = new Command("list")
     .description("Show all connected data sources")
@@ -250,7 +297,8 @@ const listSubcommand = new Command("list")
         console.log("    codify connect slack   --token xoxb-... --channels C01234");
         console.log("    codify connect github  --token ghp-... --repos owner/repo");
         console.log("    codify connect linear  --api-key lin_api_... --team ENG");
-        console.log("    codify connect notion  --token ntn_... --databases db_id\n");
+        console.log("    codify connect notion  --token ntn_... --databases db_id");
+        console.log("    codify connect docs    [path]  (default: docs/, adr/, decisions/)\n");
         return;
     }
     for (const c of connectors) {
@@ -291,6 +339,13 @@ function formatScope(entry) {
                 return dbs.join(", ");
             return "all accessible pages";
         }
+        case "docs": {
+            const dirs = entry.credentials.scanDirs;
+            if (dirs) {
+                return Array.isArray(dirs) ? dirs.join(", ") : String(dirs);
+            }
+            return "docs/, adr/, decisions/";
+        }
         default:
             return "unknown";
     }
@@ -311,11 +366,12 @@ const removeSubcommand = new Command("remove")
 });
 // ── Main connect command ──────────────────────────────────────────────
 export const connectCommand = new Command("connect")
-    .description("Connect external data sources (Slack, GitHub, Linear, Notion)")
+    .description("Connect external data sources (Slack, GitHub, Linear, Notion, Docs)")
     .addCommand(slackSubcommand)
     .addCommand(githubSubcommand)
     .addCommand(linearSubcommand)
     .addCommand(notionSubcommand)
+    .addCommand(docsSubcommand)
     .addCommand(listSubcommand)
     .addCommand(removeSubcommand);
 //# sourceMappingURL=connect.js.map

package/dist/commands/connect.js.map

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package/dist/commands/embed.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare const embedCommand: Command;
+//# sourceMappingURL=embed.d.ts.map

package/dist/commands/embed.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"embed.d.ts","sourceRoot":"","sources":["../../src/commands/embed.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAyDpC,eAAO,MAAM,YAAY,SA0JrB,CAAC"}

package/dist/commands/embed.js

@@ -0,0 +1,164 @@
+// codify embed — backfill embeddings for existing nodes using Voyage AI
+import { Command } from "commander";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
+const BATCH_SIZE = 50;
+const VOYAGE_MODEL = "voyage-3-lite";
+const VOYAGE_API_URL = "https://api.voyageai.com/v1/embeddings";
+// --- Voyage AI batch embedding ---
+async function generateBatchEmbeddings(texts, apiKey) {
+    try {
+        const response = await fetch(VOYAGE_API_URL, {
+            method: "POST",
+            headers: {
+                "Content-Type": "application/json",
+                Authorization: `Bearer ${apiKey}`,
+            },
+            body: JSON.stringify({
+                input: texts,
+                model: VOYAGE_MODEL,
+            }),
+        });
+        if (!response.ok) {
+            const body = await response.text();
+            console.error(`  Voyage API error (${response.status}): ${body}`);
+            return null;
+        }
+        const data = (await response.json());
+        if (!data.data || data.data.length !== texts.length)
+            return null;
+        const embeddings = data.data.map((d) => d.embedding);
+        if (embeddings.some((e) => !e))
+            return null;
+        return embeddings;
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        console.error(`  Voyage API request failed: ${message}`);
+        return null;
+    }
+}
+// --- Sleep helper ---
+function sleep(ms) {
+    return new Promise((resolve) => setTimeout(resolve, ms));
+}
+// --- Command definition ---
+export const embedCommand = new Command("embed")
+    .description("Backfill embeddings for nodes missing them (requires VOYAGE_API_KEY)")
+    .option("--dry-run", "Show count only, don't embed")
+    .option("--limit <n>", "Limit to N nodes")
+    .action(async (opts) => {
+    try {
+        await loadProjectConfig();
+        const { getPool, closePool } = await import("@codify/graph");
+        const pool = getPool();
+        try {
+            await pool.query("SELECT 1");
+        }
+        catch {
+            console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
+            process.exit(1);
+        }
+        const apiKey = process.env.VOYAGE_API_KEY;
+        const dryRun = !!opts.dryRun;
+        const nodeLimit = opts.limit ? parseInt(opts.limit, 10) : undefined;
+        const projectId = getProjectId();
+        // Header
+        if (dryRun) {
+            console.log("\n  Codify — Embed Nodes (dry run)\n");
+        }
+        else {
+            console.log("\n  Codify — Embed Nodes\n");
+        }
+        console.log(`  VOYAGE_API_KEY: ${apiKey ? "set" : "NOT SET"}`);
+        if (!apiKey) {
+            console.error("  ERROR: VOYAGE_API_KEY is not set. Export it: export VOYAGE_API_KEY=pa-...\n");
+            await closePool();
+            process.exit(1);
+        }
+        // Count nodes missing embeddings
+        const countResult = await pool.query("SELECT COUNT(*)::int as count FROM nodes WHERE embedding IS NULL AND superseded_by IS NULL AND project_id = $1", [projectId]);
+        const totalMissing = countResult.rows[0]?.count ?? 0;
+        const toEmbed = nodeLimit ? Math.min(nodeLimit, totalMissing) : totalMissing;
+        console.log(`  Nodes missing embeddings: ${totalMissing}`);
+        if (totalMissing === 0) {
+            console.log("\n  All nodes already have embeddings.\n");
+            await closePool();
+            return;
+        }
+        const totalBatches = Math.ceil(toEmbed / BATCH_SIZE);
+        if (dryRun) {
+            console.log(`\n  Would embed ${toEmbed} nodes in ${totalBatches} batches.\n`);
+            await closePool();
+            return;
+        }
+        // Fetch nodes missing embeddings
+        const limitClause = nodeLimit ? `LIMIT ${nodeLimit}` : "";
+        const nodesResult = await pool.query(`SELECT id, properties, metadata FROM nodes WHERE embedding IS NULL AND superseded_by IS NULL AND project_id = $1 ${limitClause}`, [projectId]);
+        const allNodes = nodesResult.rows;
+        console.log("");
+        let embedded = 0;
+        let errors = 0;
+        for (let batchIdx = 0; batchIdx < totalBatches; batchIdx++) {
+            const start = batchIdx * BATCH_SIZE;
+            const batch = allNodes.slice(start, start + BATCH_SIZE);
+            console.log(`  Batch ${batchIdx + 1}/${totalBatches} (${batch.length} nodes)...`);
+            // Build text for each node: title + description
+            const texts = batch.map((node) => {
+                const props = node.properties ?? {};
+                const meta = node.metadata ?? {};
+                const title = props.title ??
+                    meta.title ??
+                    props.name ??
+                    meta.name ??
+                    "";
+                const description = props.description ??
+                    meta.description ??
+                    props.summary ??
+                    props.reason ??
+                    "";
+                return [title, description].filter(Boolean).join(" ");
+            });
+            const embeddings = await generateBatchEmbeddings(texts, apiKey);
+            if (!embeddings) {
+                console.error(`  ERROR: Batch ${batchIdx + 1} failed. Skipping.`);
+                errors += batch.length;
+                // Still pause to respect rate limits
+                if (batchIdx < totalBatches - 1)
+                    await sleep(1000);
+                continue;
+            }
+            // Update each node with its embedding
+            for (let i = 0; i < batch.length; i++) {
+                const node = batch[i];
+                const embedding = embeddings[i];
+                const vectorStr = `[${embedding.join(",")}]`;
+                await pool.query("UPDATE nodes SET embedding = $1::vector WHERE id = $2", [vectorStr, node.id]);
+            }
+            embedded += batch.length;
+            // Pause between batches to respect rate limits
+            if (batchIdx < totalBatches - 1) {
+                await sleep(1000);
+            }
+        }
+        console.log("");
+        if (errors > 0) {
+            console.log(`  Done: ${embedded} nodes embedded, ${errors} failed.\n`);
+        }
+        else {
+            console.log(`  Done: ${embedded} nodes embedded.\n`);
+        }
+        await closePool();
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        if (message.includes("ECONNREFUSED")) {
+            console.error("\n  ERROR: Cannot connect to Codify services.");
+            console.error("  Run 'codify init' to start the infrastructure.\n");
+        }
+        else {
+            console.error(`\n  ERROR: ${message}\n`);
+        }
+        process.exit(1);
+    }
+});
+//# sourceMappingURL=embed.js.map

package/dist/commands/embed.js.map

@@ -0,0 +1 @@
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package/dist/commands/explain.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"explain.d.ts","sourceRoot":"","sources":["../../src/commands/explain.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkHpC,eAAO,MAAM,cAAc,SAwevB,CAAC"}
+{"version":3,"file":"explain.d.ts","sourceRoot":"","sources":["../../src/commands/explain.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkHpC,eAAO,MAAM,cAAc,SA4evB,CAAC"}

package/dist/commands/explain.js

@@ -3,7 +3,7 @@ import { Command } from "commander";
 import { createHash } from "node:crypto";
 import { existsSync, readFileSync, writeFileSync, mkdirSync } from "node:fs";
 import { resolve } from "node:path";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 // --- Cache helpers ---
 const CACHE_TTL_MS = 60 * 60 * 1000; // 1 hour
 function getCacheDir() {
@@ -183,15 +183,17 @@ export const explainCommand = new Command("explain")
                 return;
             }
         }
+        const projectId = getProjectId();
         // --- Search for relevant nodes ---
         // Split keywords, ILIKE against properties::text and metadata::text (same pattern as search.ts)
         const keywords = question.split(/\s+/).filter((w) => w.length > 1);
         const conditions = [
             "superseded_by IS NULL",
             "layer = ANY($1)",
+            "project_id = $2",
         ];
-        const params = [["permanent", "draft", "hot"]];
-        let paramIdx = 2;
+        const params = [["permanent", "draft", "hot"], projectId];
+        let paramIdx = 3;
         if (keywords.length > 0) {
             const keywordConditions = keywords.map((kw) => {
                 params.push(`%${kw}%`);
@@ -213,9 +215,10 @@ export const explainCommand = new Command("explain")
             "superseded_by IS NULL",
             "type = 'Gap'",
             "layer = ANY($1)",
+            "project_id = $2",
         ];
-        const gapParams = [["permanent", "draft", "hot"]];
-        let gapParamIdx = 2;
+        const gapParams = [["permanent", "draft", "hot"], projectId];
+        let gapParamIdx = 3;
         if (keywords.length > 0) {
             const gapKeywordConditions = keywords.map((kw) => {
                 gapParams.push(`%${kw}%`);

package/dist/commands/explain.js.map

@@ -1 +1 @@
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package/dist/commands/export.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"export.d.ts","sourceRoot":"","sources":["../../src/commands/export.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,eAAO,MAAM,aAAa,SAiEtB,CAAC"}
+{"version":3,"file":"export.d.ts","sourceRoot":"","sources":["../../src/commands/export.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,eAAO,MAAM,aAAa,SAwEtB,CAAC"}

package/dist/commands/export.js

@@ -2,7 +2,7 @@
 import { Command } from "commander";
 import { writeFileSync } from "node:fs";
 import { resolve } from "node:path";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 export const exportCommand = new Command("export")
     .description("Export the context graph to a JSON file")
     .option("-o, --output <file>", "Output file path")
@@ -18,10 +18,14 @@ export const exportCommand = new Command("export")
             console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
             process.exit(1);
         }
+        const projectId = getProjectId();
         // Query all active nodes (not superseded)
-        const nodesResult = await pool.query(`SELECT * FROM nodes WHERE superseded_by IS NULL ORDER BY created_at`);
-        // Query all edges
-        const edgesResult = await pool.query(`SELECT * FROM edges ORDER BY created_at`);
+        const nodesResult = await pool.query(`SELECT * FROM nodes WHERE superseded_by IS NULL AND project_id = $1 ORDER BY created_at`, [projectId]);
+        // Query all edges for this project's nodes
+        const edgesResult = await pool.query(`SELECT e.* FROM edges e
+         JOIN nodes n ON n.id = e.source_id
+         WHERE n.project_id = $1
+         ORDER BY e.created_at`, [projectId]);
         const nodes = nodesResult.rows;
         const edges = edgesResult.rows;
         // Determine output filename

package/dist/commands/export.js.map

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package/dist/commands/gaps.d.ts.map

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