@codified/cli 0.3.9 → 0.4.0

package/dist/commands/gaps.js

@@ -1,6 +1,6 @@
 // codify gaps — show gaps detected by the Gap Engine
 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";
@@ -95,6 +95,7 @@ export const gapsCommand = new Command("gaps")
     .option("--severity <level>", "Filter by severity: critical, high, medium, low")
     .option("--limit <n>", "Maximum gaps to show", "10")
     .option("--status <status>", "Filter by status: detected, acknowledged, collection_in_progress, resolved, wont_fix")
+    .option("--sort <method>", "Sort order: priority, freshness, created (default: freshness)")
     .action(async (opts) => {
     try {
         await loadProjectConfig();
@@ -107,13 +108,15 @@ export const gapsCommand = new Command("gaps")
             console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
             process.exit(1);
         }
+        const projectId = getProjectId();
         // Build query with filters
         const conditions = [
             "type = 'Gap'",
             "superseded_by IS NULL",
+            "project_id = $1",
         ];
-        const params = [];
-        let paramIdx = 1;
+        const params = [projectId];
+        let paramIdx = 2;
         if (opts.severity) {
             const valid = ["critical", "high", "medium", "low"];
             if (!valid.includes(opts.severity)) {
@@ -137,23 +140,49 @@ export const gapsCommand = new Command("gaps")
             console.error("\n  ERROR: --limit must be a positive integer.\n");
             process.exit(1);
         }
+        // Validate --sort flag
+        const sortMethod = opts.sort ?? "freshness";
+        const validSorts = ["priority", "freshness", "created"];
+        if (!validSorts.includes(sortMethod)) {
+            console.error(`\n  ERROR: Invalid sort method "${sortMethod}". Use: ${validSorts.join(", ")}\n`);
+            process.exit(1);
+        }
         // Fetch more gaps than requested to have enough after dedup.
         // We fetch up to 5x the limit so dedup can remove duplicates and still fill the page.
         const fetchLimit = limit * 5;
-        // Query gaps sorted by severity priority, then by creation date (newest first)
-        const gapsResult = await pool.query(`SELECT id, properties, metadata, freshness, confidence, created_at, updated_at
+        // Build sort-dependent query
+        let gapsQuery;
+        if (sortMethod === "priority") {
+            // Priority = severity weight x affected node count (triggered edges)
+            const where = conditions.map(c => `n.${c}`).join(" AND ");
+            gapsQuery = `SELECT n.id, n.properties, n.metadata, n.freshness, n.confidence, n.created_at, n.updated_at,
+           (CASE n.properties->>'severity'
+             WHEN 'critical' THEN 4 WHEN 'high' THEN 3 WHEN 'medium' THEN 2 WHEN 'low' THEN 1 ELSE 0
+           END) * GREATEST(1, (
+             SELECT COUNT(*) FROM edges e
+             WHERE e.target_id = n.id AND e.type = 'triggered' AND e.branch_id IS NULL
+           )) AS priority_score
+         FROM nodes n
+         WHERE ${where}
+         ORDER BY priority_score DESC, n.created_at DESC
+         LIMIT $${paramIdx}`;
+        }
+        else if (sortMethod === "created") {
+            gapsQuery = `SELECT id, properties, metadata, freshness, confidence, created_at, updated_at
+         FROM nodes
+         WHERE ${conditions.join(" AND ")}
+         ORDER BY created_at DESC
+         LIMIT $${paramIdx}`;
+        }
+        else {
+            // freshness (default): stalest first
+            gapsQuery = `SELECT id, properties, metadata, freshness, confidence, created_at, updated_at
          FROM nodes
          WHERE ${conditions.join(" AND ")}
-         ORDER BY
-           CASE properties->>'severity'
-             WHEN 'critical' THEN 0
-             WHEN 'high' THEN 1
-             WHEN 'medium' THEN 2
-             WHEN 'low' THEN 3
-             ELSE 4
-           END ASC,
-           created_at DESC
-         LIMIT $${paramIdx}`, [...params, fetchLimit]);
+         ORDER BY freshness ASC
+         LIMIT $${paramIdx}`;
+        }
+        const gapsResult = await pool.query(gapsQuery, [...params, fetchLimit]);
         const allGaps = gapsResult.rows;
         // Header
         console.log(`\n  ${BOLD}Codify — Gap Report${RESET}\n`);
@@ -210,23 +239,30 @@ export const gapsCommand = new Command("gaps")
                 seen.set(dedupKey, gap);
             }
         }
-        // Re-sort deduped gaps by severity then created_at (same order as the query)
+        // Re-sort deduped gaps to match the chosen sort order
         const dedupedGaps = [...seen.values()].sort((a, b) => {
-            const sevA = SEVERITY_ORDER[a.properties.severity ?? ""] ?? 4;
-            const sevB = SEVERITY_ORDER[b.properties.severity ?? ""] ?? 4;
-            if (sevA !== sevB)
-                return sevA - sevB;
-            return new Date(b.created_at).getTime() - new Date(a.created_at).getTime();
+            if (sortMethod === "priority") {
+                const scoreA = a.priority_score ?? 0;
+                const scoreB = b.priority_score ?? 0;
+                if (scoreA !== scoreB)
+                    return scoreB - scoreA;
+                return new Date(b.created_at).getTime() - new Date(a.created_at).getTime();
+            }
+            if (sortMethod === "created") {
+                return new Date(b.created_at).getTime() - new Date(a.created_at).getTime();
+            }
+            // freshness: stalest first (ascending)
+            return (a.freshness ?? 1) - (b.freshness ?? 1);
         });
         // Apply the user's limit after dedup
         const gaps = dedupedGaps.slice(0, limit);
         // Summary line
         const totalResult = await pool.query(`SELECT COUNT(*) as count FROM nodes
-         WHERE type = 'Gap' AND superseded_by IS NULL`);
+         WHERE type = 'Gap' AND superseded_by IS NULL AND project_id = $1`, [projectId]);
         const total = parseInt(totalResult.rows[0].count, 10);
         const severityCounts = await pool.query(`SELECT properties->>'severity' as severity, COUNT(*) as count
-         FROM nodes WHERE type = 'Gap' AND superseded_by IS NULL
-         GROUP BY properties->>'severity' ORDER BY count DESC`);
+         FROM nodes WHERE type = 'Gap' AND superseded_by IS NULL AND project_id = $1
+         GROUP BY properties->>'severity' ORDER BY count DESC`, [projectId]);
         const countParts = [];
         for (const row of severityCounts.rows) {
             const sev = row.severity ?? "unknown";
@@ -292,7 +328,7 @@ export const gapsCommand = new Command("gaps")
             console.log("");
         }
         // Footer help
-        console.log(`  ${DIM}Flags: --severity critical|high|medium|low  --status detected|resolved  --limit <n>${RESET}`);
+        console.log(`  ${DIM}Flags: --severity critical|high|medium|low  --status detected|resolved  --limit <n>  --sort priority|freshness|created${RESET}`);
         console.log("");
         await closePool();
     }

package/dist/commands/gaps.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA4EpC,eAAO,MAAM,YAAY,SAoRrB,CAAC"}
+{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA4EpC,eAAO,MAAM,YAAY,SAwRrB,CAAC"}

package/dist/commands/graph.js

@@ -1,6 +1,6 @@
 // codify graph — Mermaid diagram visualization of the context graph
 import { Command } from "commander";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 import { writeFileSync } from "node:fs";
 // --- Color helpers (ANSI escape codes) ---
 const RESET = "\x1b[0m";
@@ -101,13 +101,15 @@ export const graphCommand = new Command("graph")
             console.error("\n  ERROR: --limit must be a positive integer.\n");
             process.exit(1);
         }
+        const projectId = getProjectId();
         // Step 1: Find seed nodes via ILIKE keyword search
         const seedConditions = [
             "superseded_by IS NULL",
             "layer = ANY($1)",
+            "project_id = $2",
         ];
-        const seedParams = [["permanent", "draft", "hot"]];
-        let paramIdx = 2;
+        const seedParams = [["permanent", "draft", "hot"], projectId];
+        let paramIdx = 3;
         const keywords = queryStr.split(/\s+/).filter((w) => w.length > 1);
         if (keywords.length > 0) {
             const keywordConditions = keywords.map((kw) => {
@@ -174,7 +176,8 @@ export const graphCommand = new Command("graph")
              (e.target_id = ANY($1::uuid[]) AND n.id = e.source_id)
            )
            WHERE (e.source_id = ANY($1::uuid[]) OR e.target_id = ANY($1::uuid[]))
-             AND n.superseded_by IS NULL`, [frontierIds]);
+             AND n.superseded_by IS NULL
+             AND n.project_id = $2`, [frontierIds, projectId]);
             for (const row of edgeResult.rows) {
                 // Always record edges between known nodes
                 edgeList.push({

package/dist/commands/graph.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"import-cmd.d.ts","sourceRoot":"","sources":["../../src/commands/import-cmd.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,eAAO,MAAM,aAAa,SAuNtB,CAAC"}
+{"version":3,"file":"import-cmd.d.ts","sourceRoot":"","sources":["../../src/commands/import-cmd.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,eAAO,MAAM,aAAa,SA2NtB,CAAC"}

package/dist/commands/import-cmd.js

@@ -3,7 +3,7 @@
 import { Command } from "commander";
 import { readFileSync } from "node:fs";
 import { resolve } from "node:path";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 export const importCommand = new Command("import")
     .description("Import a context graph from a JSON backup file")
     .argument("<file>", "Path to the JSON export file")
@@ -58,6 +58,7 @@ export const importCommand = new Command("import")
             // Determine conflict strategy
             const isUpsert = !opts.merge && !opts.replace;
             const isMerge = !!opts.merge;
+            const projectId = getProjectId();
             // ── Import nodes ───────────────────────────────────────────────
             console.log(`\n  Importing ${nodes.length} nodes...`);
             for (const node of nodes) {
@@ -79,6 +80,7 @@ export const importCommand = new Command("import")
                     node.version ?? 1,
                     node.created_at,
                     node.updated_at,
+                    projectId,
                 ];
                 if (opts.replace || isMerge) {
                     // For replace mode: straight insert (table was truncated)
@@ -88,12 +90,12 @@ export const importCommand = new Command("import")
                 id, type, layer, branch_id, confidence, freshness,
                 properties, metadata, tags, source_system, source_reference,
                 source_agent_id, source_reliability, superseded_by, version,
-                created_at, updated_at
+                created_at, updated_at, project_id
               ) VALUES (
                 $1, $2, $3, $4, $5, $6,
                 $7::jsonb, $8::jsonb, $9, $10, $11,
                 $12, $13, $14, $15,
-                $16, $17
+                $16, $17, $18
               ) ${conflictClause}`, values);
                 }
                 else if (isUpsert) {
@@ -102,12 +104,12 @@ export const importCommand = new Command("import")
                 id, type, layer, branch_id, confidence, freshness,
                 properties, metadata, tags, source_system, source_reference,
                 source_agent_id, source_reliability, superseded_by, version,
-                created_at, updated_at
+                created_at, updated_at, project_id
               ) VALUES (
                 $1, $2, $3, $4, $5, $6,
                 $7::jsonb, $8::jsonb, $9, $10, $11,
                 $12, $13, $14, $15,
-                $16, $17
+                $16, $17, $18
               ) ON CONFLICT (id) DO UPDATE SET
                 type = EXCLUDED.type,
                 layer = EXCLUDED.layer,
@@ -124,7 +126,8 @@ export const importCommand = new Command("import")
                 superseded_by = EXCLUDED.superseded_by,
                 version = EXCLUDED.version,
                 created_at = EXCLUDED.created_at,
-                updated_at = EXCLUDED.updated_at`, values);
+                updated_at = EXCLUDED.updated_at,
+                project_id = EXCLUDED.project_id`, values);
                 }
             }
             // ── Import edges ───────────────────────────────────────────────

package/dist/commands/import-cmd.js.map

@@ -1 +1 @@
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package/dist/commands/refresh-freshness.d.ts

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

package/dist/commands/refresh-freshness.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"refresh-freshness.d.ts","sourceRoot":"","sources":["../../src/commands/refresh-freshness.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAUpC,eAAO,MAAM,uBAAuB,SA0HhC,CAAC"}

package/dist/commands/refresh-freshness.js

@@ -0,0 +1,90 @@
+// codify refresh-freshness — recalculate freshness scores for all nodes
+import { Command } from "commander";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
+// --- ANSI color helpers ---
+const RESET = "\x1b[0m";
+const BOLD = "\x1b[1m";
+const DIM = "\x1b[2m";
+const GREEN = "\x1b[32m";
+export const refreshFreshnessCommand = new Command("refresh-freshness")
+    .description("Recalculate freshness scores for all nodes")
+    .action(async () => {
+    try {
+        await loadProjectConfig();
+        const { getPool, closePool, calculateFreshness, countCorroboration } = 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 projectId = getProjectId();
+        console.log(`\n  ${BOLD}Codify — Refresh Freshness Scores${RESET}\n`);
+        // Fetch all non-superseded nodes for the current project
+        const nodesResult = await pool.query(`SELECT id, type, updated_at, source_reliability, freshness
+         FROM nodes
+         WHERE superseded_by IS NULL AND project_id = $1`, [projectId]);
+        const nodes = nodesResult.rows;
+        const totalNodes = nodes.length;
+        if (totalNodes === 0) {
+            console.log("  No nodes found in the graph.\n");
+            await closePool();
+            return;
+        }
+        console.log(`  Processing ${totalNodes} nodes...`);
+        const now = new Date();
+        let updatedCount = 0;
+        const updatedNodeIds = [];
+        for (const node of nodes) {
+            const corroborationCount = await countCorroboration(node.id);
+            const newFreshness = calculateFreshness({
+                nodeType: node.type,
+                lastUpdated: new Date(node.updated_at),
+                corroborationCount,
+                sourceReliability: node.source_reliability,
+                now,
+            });
+            // Always write the recalculated value
+            if (Math.abs(newFreshness - node.freshness) > 0.001) {
+                await pool.query(`UPDATE nodes SET freshness = $1 WHERE id = $2`, [newFreshness, node.id]);
+                updatedCount++;
+                updatedNodeIds.push(node.id);
+            }
+        }
+        console.log(`  Updated ${GREEN}${BOLD}${updatedCount}${RESET} freshness scores.\n`);
+        // Write metabolism_audit entry
+        // Check if the table exists first
+        const tableCheck = await pool.query("SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'metabolism_audit') as exists");
+        if (tableCheck.rows[0].exists) {
+            await pool.query(`INSERT INTO metabolism_audit (event_type, node_ids, action, reason, metadata)
+           VALUES ($1, $2, $3, $4, $5)`, [
+                "freshness_refresh",
+                updatedNodeIds.length > 0 ? updatedNodeIds : [],
+                "refreshed",
+                `Manual freshness refresh: ${updatedCount} of ${totalNodes} nodes updated`,
+                JSON.stringify({
+                    total_nodes: totalNodes,
+                    updated_count: updatedCount,
+                    triggered_by: "cli",
+                    timestamp: now.toISOString(),
+                }),
+            ]);
+            console.log(`  ${DIM}Audit trail recorded.${RESET}\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=refresh-freshness.js.map

package/dist/commands/refresh-freshness.js.map

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

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