@codified/cli 0.3.9 → 0.4.0

package/dist/commands/bootstrap.js

@@ -1,14 +1,15 @@
-// codify bootstrap — mine the current project's git history into the context graph
+// codify bootstrap — mine the current project's git history and documents into the context graph
 //
 // Uses the ingest service: LocalGitConnector → GitMiner (Claude-powered) → StagingPipeline
 // This is the proper pipeline — Claude interprets commit messages, PR descriptions,
-// and review comments to extract Decision, Feature, CodeArtifact, Discussion, Person nodes.
+// review comments, and markdown documents to extract Decision, Feature, CodeArtifact,
+// Discussion, Person nodes.
 import { Command } from "commander";
 import { spawnSync } from "node:child_process";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, loadConnectors } from "../lib/config.js";
 import { confirm } from "../lib/prompt.js";
 export const bootstrapCommand = new Command("bootstrap")
-    .description("Mine the current project's git history into the context graph")
+    .description("Mine git history and connected documents into the context graph")
     .option("--limit <n>", "Maximum commits to process", "500")
     .option("--skip-prs", "Skip GitHub PR fetching")
     .option("--batch-size <n>", "Artifacts per miner batch", "10")
@@ -111,13 +112,51 @@ export const bootstrapCommand = new Command("bootstrap")
         console.log = patchedLog;
         const result = await ingest.bootstrap.run("local-git");
         console.log = originalLog;
+        let totalArtifacts = result.totalArtifacts;
+        let totalCreated = result.pipeline.created.length;
+        let totalMerged = result.pipeline.merged.length;
+        let totalRejected = result.pipeline.rejected.length;
+        // Check for registered docs connectors and run them too
+        const connectors = loadConnectors();
+        const docsConnectors = connectors.filter((c) => c.type === "docs");
+        if (docsConnectors.length > 0) {
+            console.log("\n  [3/3] Mining markdown documents with Claude...\n");
+            for (const docsEntry of docsConnectors) {
+                const scanDirs = docsEntry.credentials.scanDirs;
+                const authCredentials = {
+                    basePath: docsEntry.credentials.basePath ?? cwd,
+                };
+                if (scanDirs) {
+                    authCredentials.scanDirs = Array.isArray(scanDirs)
+                        ? scanDirs.join(",")
+                        : String(scanDirs);
+                }
+                try {
+                    await ingest.registry.connect("markdown", {
+                        type: "docs",
+                        credentials: authCredentials,
+                    });
+                    const docsResult = await ingest.bootstrap.run("markdown");
+                    totalArtifacts += docsResult.totalArtifacts;
+                    totalCreated += docsResult.pipeline.created.length;
+                    totalMerged += docsResult.pipeline.merged.length;
+                    totalRejected += docsResult.pipeline.rejected.length;
+                    console.log(`  Documents: ${docsResult.totalArtifacts} files mined, ` +
+                        `${docsResult.pipeline.created.length} nodes created`);
+                }
+                catch (err) {
+                    const msg = err instanceof Error ? err.message : String(err);
+                    console.warn(`  WARN: Document mining failed: ${msg}`);
+                }
+            }
+        }
         const durationSec = ((Date.now() - startTime) / 1000).toFixed(1);
         // Summary
         console.log(`\n  Your context graph is live!\n`);
-        console.log(`  ${result.totalArtifacts} artifacts mined in ${durationSec}s\n`);
-        console.log(`  Nodes: ${result.pipeline.created.length} created, ${result.pipeline.merged.length} merged`);
-        if (result.pipeline.rejected.length > 0) {
-            console.log(`  Skipped: ${result.pipeline.rejected.length}`);
+        console.log(`  ${totalArtifacts} artifacts mined in ${durationSec}s\n`);
+        console.log(`  Nodes: ${totalCreated} created, ${totalMerged} merged`);
+        if (totalRejected > 0) {
+            console.log(`  Skipped: ${totalRejected}`);
         }
         console.log(`\n  Run 'codify status' to see your graph.`);
         console.log(`  Claude Code now has full context about your project.\n`);

package/dist/commands/bootstrap.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwEpC,eAAO,MAAM,YAAY,SAwSrB,CAAC"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwEpC,eAAO,MAAM,YAAY,SA0SrB,CAAC"}

package/dist/commands/check.js

@@ -1,6 +1,6 @@
 // codify check — context check for code review / CI gating
 import { Command } from "commander";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 // --- Color helpers (ANSI escape codes) ---
 const RESET = "\x1b[0m";
 const BOLD = "\x1b[1m";
@@ -93,10 +93,11 @@ export const checkCommand = new Command("check")
             await closePool();
             process.exit(0);
         }
+        const projectId = getProjectId();
         // Build ILIKE conditions for keywords
-        const conditions = ["superseded_by IS NULL"];
-        const params = [];
-        let paramIdx = 1;
+        const conditions = ["superseded_by IS NULL", "project_id = $1"];
+        const params = [projectId];
+        let paramIdx = 2;
         const keywordConditions = keywords.map((kw) => {
             params.push(`%${kw}%`);
             const idx = paramIdx++;

package/dist/commands/check.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"cleanup.d.ts","sourceRoot":"","sources":["../../src/commands/cleanup.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkNpC,eAAO,MAAM,cAAc,SAEE,CAAC"}
+{"version":3,"file":"cleanup.d.ts","sourceRoot":"","sources":["../../src/commands/cleanup.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA6cpC,eAAO,MAAM,cAAc,SAIC,CAAC"}

package/dist/commands/cleanup.js

@@ -1,6 +1,6 @@
 // codify cleanup gaps — fix legacy gap descriptions containing UUIDs
 import { Command } from "commander";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 // --- Color helpers (ANSI escape codes) ---
 const RESET = "\x1b[0m";
 const BOLD = "\x1b[1m";
@@ -46,8 +46,9 @@ const gapsSubcommand = new Command("gaps")
         else {
             console.log(`\n  ${BOLD}Codify — Cleanup Gap Descriptions${RESET}\n`);
         }
+        const projectId = getProjectId();
         // Fetch all active Gap nodes
-        const gapsResult = await pool.query(`SELECT id, properties, metadata FROM nodes WHERE type = 'Gap' AND superseded_by IS NULL`);
+        const gapsResult = await pool.query(`SELECT id, properties, metadata FROM nodes WHERE type = 'Gap' AND superseded_by IS NULL AND project_id = $1`, [projectId]);
         const gaps = gapsResult.rows;
         if (gaps.length === 0) {
             console.log("  No gaps found in the graph.\n");
@@ -159,8 +160,209 @@ const gapsSubcommand = new Command("gaps")
         process.exit(1);
     }
 });
+// --- Subcommand: nodes ---
+// Patterns that indicate a title is a hash or UUID rather than a meaningful name
+const UUID_TITLE_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
+const HASH_TITLE_RE = /^[0-9a-f]{7,40}$/i;
+function looksLikeHashOrUuid(title) {
+    return UUID_TITLE_RE.test(title.trim()) || HASH_TITLE_RE.test(title.trim());
+}
+/**
+ * For CodeArtifact nodes, try to find a file path from properties/metadata.
+ * Returns a short, human-readable title derived from the path, or null.
+ */
+function extractCodeArtifactTitle(properties, metadata) {
+    const p = properties ?? {};
+    const m = metadata ?? {};
+    // Priority order for file path sources
+    const candidates = [
+        p.path,
+        p.filePath,
+        m.path,
+        m.filePath,
+        m.source_reference,
+    ];
+    for (const candidate of candidates) {
+        if (typeof candidate === "string" && candidate.length > 0) {
+            // Use the path as-is if short enough, otherwise use last meaningful segment(s)
+            const trimmed = candidate.replace(/^\/+|\/+$/g, "");
+            if (trimmed.length <= 60)
+                return trimmed;
+            // Take last two path segments for context
+            const parts = trimmed.split("/");
+            if (parts.length >= 2) {
+                return parts.slice(-2).join("/");
+            }
+            return parts[parts.length - 1];
+        }
+    }
+    return null;
+}
+/**
+ * For non-CodeArtifact nodes, try to find a better title from description/name fields.
+ */
+function extractGenericTitle(properties, metadata) {
+    const p = properties ?? {};
+    const m = metadata ?? {};
+    const candidates = [
+        p.name,
+        m.name,
+        p.description,
+        m.description,
+    ];
+    for (const candidate of candidates) {
+        if (typeof candidate === "string" && candidate.length > 0) {
+            // Don't use a name/description that is itself a hash or UUID
+            if (looksLikeHashOrUuid(candidate))
+                continue;
+            // Truncate long descriptions to something reasonable for a title
+            if (candidate.length > 80)
+                return candidate.slice(0, 77) + "...";
+            return candidate;
+        }
+    }
+    return null;
+}
+async function runNodesCleanup(opts) {
+    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 isDryRun = !!opts.dryRun;
+    if (isDryRun) {
+        console.log(`\n  ${BOLD}Codify — Cleanup Node Titles (dry run)${RESET}\n`);
+    }
+    else {
+        console.log(`\n  ${BOLD}Codify — Cleanup Node Titles${RESET}\n`);
+    }
+    console.log(`  Scanning for nodes with hash/UUID titles...\n`);
+    const projectId = getProjectId();
+    // Fetch all non-Gap nodes that are not superseded
+    const nodesResult = await pool.query(`SELECT id, type, properties, metadata FROM nodes WHERE type != 'Gap' AND superseded_by IS NULL AND project_id = $1`, [projectId]);
+    const allNodes = nodesResult.rows;
+    // Filter to nodes whose title looks like a hash or UUID
+    const candidates = [];
+    for (const node of allNodes) {
+        const title = (node.properties ?? {}).title ?? "";
+        if (title.length > 0 && looksLikeHashOrUuid(title)) {
+            candidates.push(node);
+        }
+    }
+    if (candidates.length === 0) {
+        console.log("  No nodes with hash/UUID titles found.\n");
+        await closePool();
+        return { fixed: 0, skipped: 0 };
+    }
+    // Group by type for reporting
+    const byType = new Map();
+    for (const node of candidates) {
+        const list = byType.get(node.type) ?? [];
+        list.push(node);
+        byType.set(node.type, list);
+    }
+    let totalFixed = 0;
+    let totalSkipped = 0;
+    for (const [type, nodes] of byType) {
+        const fixes = [];
+        let skippedInType = 0;
+        for (const node of nodes) {
+            const oldTitle = (node.properties ?? {}).title ?? "";
+            let newTitle = null;
+            if (type === "CodeArtifact") {
+                newTitle = extractCodeArtifactTitle(node.properties, node.metadata);
+            }
+            // If CodeArtifact extraction failed, or if this is another type, try generic fallback
+            if (newTitle === null) {
+                newTitle = extractGenericTitle(node.properties, node.metadata);
+            }
+            if (newTitle === null || looksLikeHashOrUuid(newTitle)) {
+                skippedInType++;
+                continue;
+            }
+            fixes.push({ oldTitle, newTitle, id: node.id });
+            if (!isDryRun) {
+                await pool.query(`UPDATE nodes SET properties = jsonb_set(properties, '{title}', $2::jsonb), updated_at = now() WHERE id = $1`, [node.id, JSON.stringify(newTitle)]);
+            }
+        }
+        if (fixes.length > 0) {
+            const verb = isDryRun ? "Would fix" : "Fixed";
+            console.log(`  ${verb} ${GREEN}${fixes.length}${RESET} of ${nodes.length} ${CYAN}${type}${RESET} nodes:`);
+            for (const fix of fixes) {
+                const oldDisplay = fix.oldTitle.length > 20 ? fix.oldTitle.slice(0, 17) + "..." : fix.oldTitle;
+                console.log(`    ${DIM}"${oldDisplay}"${RESET} ${DIM}->${RESET} ${GREEN}"${fix.newTitle}"${RESET}`);
+            }
+            console.log("");
+        }
+        if (skippedInType > 0) {
+            totalSkipped += skippedInType;
+        }
+        totalFixed += fixes.length;
+    }
+    if (totalSkipped > 0) {
+        console.log(`  Skipped ${YELLOW}${totalSkipped}${RESET} node${totalSkipped === 1 ? "" : "s"} (no better title available).\n`);
+    }
+    // Summary
+    if (isDryRun) {
+        console.log(`  ${YELLOW}Dry run:${RESET} ${totalFixed} title${totalFixed === 1 ? "" : "s"} would be fixed.\n`);
+    }
+    else {
+        console.log(`  Summary: ${BOLD}${totalFixed}${RESET} title${totalFixed === 1 ? "" : "s"} fixed.\n`);
+    }
+    await closePool();
+    return { fixed: totalFixed, skipped: totalSkipped };
+}
+const nodesSubcommand = new Command("nodes")
+    .description("Fix node titles that are hashes or UUIDs instead of meaningful names")
+    .option("--dry-run", "Show what would be fixed without making changes")
+    .action(async (opts) => {
+    try {
+        await runNodesCleanup(opts);
+    }
+    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);
+    }
+});
+// --- Subcommand: all ---
+const allSubcommand = new Command("all")
+    .description("Run all cleanup tasks (gaps + nodes)")
+    .option("--dry-run", "Show what would be fixed without making changes")
+    .action(async (opts) => {
+    try {
+        // Run gaps cleanup first
+        await gapsSubcommand.parseAsync(opts.dryRun ? ["gaps", "--dry-run"] : ["gaps"], { from: "user" });
+        // Then run nodes cleanup
+        await runNodesCleanup(opts);
+    }
+    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);
+    }
+});
 // --- Parent command ---
 export const cleanupCommand = new Command("cleanup")
     .description("Fix legacy data quality issues")
-    .addCommand(gapsSubcommand);
+    .addCommand(gapsSubcommand)
+    .addCommand(nodesSubcommand)
+    .addCommand(allSubcommand);
 //# sourceMappingURL=cleanup.js.map

package/dist/commands/cleanup.js.map

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package/dist/commands/collect.d.ts

@@ -13,7 +13,7 @@ export declare function collectEvidenceForGap(pool: {
     id: string;
     type: string;
     title: string;
-}>): Promise<{
+}>, projectId?: string): Promise<{
     evidenceNodes: Array<{
         id: string;
         type: string;

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

@@ -1 +1 @@
-{"version":3,"file":"collect.d.ts","sourceRoot":"","sources":["../../src/commands/collect.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAmDpC;;;;;GAKG;AACH,wBAAsB,qBAAqB,CACzC,IAAI,EAAE;IACJ,KAAK,EAAE,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACjE,GAAG,EAAE,MAAM,EACX,MAAM,CAAC,EAAE,OAAO,EAAE,KACf,OAAO,CAAC;QAAE,IAAI,EAAE,CAAC,EAAE,CAAA;KAAE,CAAC,CAAC;CAC7B,EACD,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,KAAK,CAAC;IACnB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;CACf,CAAC,GACD,OAAO,CAAC;IACT,aAAa,EAAE,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACxF,YAAY,EAAE,MAAM,CAAC;CACtB,CAAC,CA2FD;AAID,eAAO,MAAM,cAAc,SAiLvB,CAAC"}
+{"version":3,"file":"collect.d.ts","sourceRoot":"","sources":["../../src/commands/collect.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAmDpC;;;;;GAKG;AACH,wBAAsB,qBAAqB,CACzC,IAAI,EAAE;IACJ,KAAK,EAAE,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACjE,GAAG,EAAE,MAAM,EACX,MAAM,CAAC,EAAE,OAAO,EAAE,KACf,OAAO,CAAC;QAAE,IAAI,EAAE,CAAC,EAAE,CAAA;KAAE,CAAC,CAAC;CAC7B,EACD,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,KAAK,CAAC;IACnB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;CACf,CAAC,EACF,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC;IACT,aAAa,EAAE,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACxF,YAAY,EAAE,MAAM,CAAC;CACtB,CAAC,CAgGD;AAID,eAAO,MAAM,cAAc,SAsLvB,CAAC"}

package/dist/commands/collect.js

@@ -1,6 +1,6 @@
 // codify collect — mine the graph for evidence that addresses gaps
 import { Command } from "commander";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 // --- Color helpers (ANSI escape codes) ---
 const RESET = "\x1b[0m";
 const BOLD = "\x1b[1m";
@@ -51,7 +51,7 @@ function extractKeywords(title) {
  *
  * Exported so triage.ts can reuse it inline.
  */
-export async function collectEvidenceForGap(pool, gapId, affectedNodes) {
+export async function collectEvidenceForGap(pool, gapId, affectedNodes, projectId) {
     const evidenceNodes = [];
     let edgesCreated = 0;
     // Collect IDs already connected to the gap (to exclude them from results)
@@ -75,6 +75,10 @@ export async function collectEvidenceForGap(pool, gapId, affectedNodes) {
         ];
         const params = [["permanent", "draft"]];
         let paramIdx = 2;
+        if (projectId) {
+            conditions.push(`project_id = $${paramIdx++}`);
+            params.push(projectId);
+        }
         const keywordConditions = keywords.map((kw) => {
             params.push(`%${kw}%`);
             const idx = paramIdx++;
@@ -138,6 +142,7 @@ export const collectCommand = new Command("collect")
             console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
             process.exit(1);
         }
+        const projectId = getProjectId();
         // Determine which gaps to process
         let gapsSql;
         let gapsParams;
@@ -145,8 +150,8 @@ export const collectCommand = new Command("collect")
             // Specific gap
             gapsSql = `SELECT id, properties, metadata
            FROM nodes
-           WHERE id = $1 AND type = 'Gap' AND superseded_by IS NULL`;
-            gapsParams = [opts.gap];
+           WHERE id = $1 AND type = 'Gap' AND superseded_by IS NULL AND project_id = $2`;
+            gapsParams = [opts.gap, projectId];
         }
         else {
             // Top N unresolved gaps by severity, then freshness
@@ -160,6 +165,7 @@ export const collectCommand = new Command("collect")
            WHERE type = 'Gap'
              AND superseded_by IS NULL
              AND COALESCE(properties->>'status', 'detected') NOT IN ('resolved', 'wont_fix')
+             AND project_id = $1
            ORDER BY
              CASE properties->>'severity'
                WHEN 'critical' THEN 0
@@ -169,8 +175,8 @@ export const collectCommand = new Command("collect")
                ELSE 4
              END ASC,
              freshness DESC
-           LIMIT $1`;
-            gapsParams = [limit];
+           LIMIT $2`;
+            gapsParams = [projectId, limit];
         }
         const gapsResult = await pool.query(gapsSql, gapsParams);
         const gaps = gapsResult.rows;
@@ -198,7 +204,8 @@ export const collectCommand = new Command("collect")
            WHERE (e.source_id = $1 OR e.target_id = $1)
              AND n.id != $1
              AND n.superseded_by IS NULL
-           GROUP BY n.id, n.type, n.properties, n.metadata`, [gap.id]);
+             AND n.project_id = $2
+           GROUP BY n.id, n.type, n.properties, n.metadata`, [gap.id, projectId]);
             const affectedNodes = affectedResult.rows.map((r) => {
                 const p = r.properties ?? {};
                 const m = r.metadata ?? {};
@@ -224,7 +231,7 @@ export const collectCommand = new Command("collect")
                 continue;
             }
             // Run the graph mining
-            const { evidenceNodes, edgesCreated } = await collectEvidenceForGap(pool, gap.id, affectedNodes);
+            const { evidenceNodes, edgesCreated } = await collectEvidenceForGap(pool, gap.id, affectedNodes, projectId);
             if (evidenceNodes.length > 0) {
                 console.log(`    ${GREEN}Found ${evidenceNodes.length} relevant node${evidenceNodes.length === 1 ? "" : "s"}:${RESET}`);
                 for (const ev of evidenceNodes) {

package/dist/commands/collect.js.map

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

@@ -1 +1 @@
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