@optave/codegraph 3.1.4 → 3.1.5

package/src/cli/commands/deps.js

@@ -1,4 +1,4 @@
-import { fileDeps } from '../../queries-cli.js';
+import { fileDeps } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'deps <file>',
@@ -6,11 +6,7 @@ export const command = {
   queryOpts: true,
   execute([file], opts, ctx) {
     fileDeps(file, opts.db, {
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/diff-impact.js

@@ -1,4 +1,4 @@
-import { diffImpact } from '../../queries-cli.js';
+import { diffImpact } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'diff-impact [ref]',
@@ -19,12 +19,8 @@ export const command = {
       ref,
       staged: opts.staged,
       depth: parseInt(opts.depth, 10),
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
       format: opts.format,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/embed.js

@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { buildEmbeddings, DEFAULT_MODEL, EMBEDDING_STRATEGIES } from '../../embeddings/index.js';
+import { buildEmbeddings, DEFAULT_MODEL, EMBEDDING_STRATEGIES } from '../../domain/search/index.js';
 
 export const command = {
   name: 'embed [dir]',

package/src/cli/commands/export.js

@@ -1,5 +1,4 @@
 import fs from 'node:fs';
-import { openReadonlyOrFail } from '../../db.js';
 import {
   exportDOT,
   exportGraphML,
@@ -7,7 +6,8 @@ import {
   exportJSON,
   exportMermaid,
   exportNeo4jCSV,
-} from '../../export.js';
+} from '../../features/export.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'export',
@@ -23,7 +23,7 @@ export const command = {
     ['-o, --output <file>', 'Write to file instead of stdout'],
   ],
   execute(_args, opts, ctx) {
-    const db = openReadonlyOrFail(opts.db);
+    const { db, close } = openGraph(opts);
     const exportOpts = {
       fileLevel: !opts.functions,
       noTests: ctx.resolveNoTests(opts),
@@ -32,38 +32,41 @@ export const command = {
     };
 
     let output;
-    switch (opts.format) {
-      case 'mermaid':
-        output = exportMermaid(db, exportOpts);
-        break;
-      case 'json':
-        output = JSON.stringify(exportJSON(db, exportOpts), null, 2);
-        break;
-      case 'graphml':
-        output = exportGraphML(db, exportOpts);
-        break;
-      case 'graphson':
-        output = JSON.stringify(exportGraphSON(db, exportOpts), null, 2);
-        break;
-      case 'neo4j': {
-        const csv = exportNeo4jCSV(db, exportOpts);
-        if (opts.output) {
-          const base = opts.output.replace(/\.[^.]+$/, '') || opts.output;
-          fs.writeFileSync(`${base}-nodes.csv`, csv.nodes, 'utf-8');
-          fs.writeFileSync(`${base}-relationships.csv`, csv.relationships, 'utf-8');
-          db.close();
-          console.log(`Exported to ${base}-nodes.csv and ${base}-relationships.csv`);
-          return;
+    try {
+      switch (opts.format) {
+        case 'mermaid':
+          output = exportMermaid(db, exportOpts);
+          break;
+        case 'json':
+          output = JSON.stringify(exportJSON(db, exportOpts), null, 2);
+          break;
+        case 'graphml':
+          output = exportGraphML(db, exportOpts);
+          break;
+        case 'graphson':
+          output = JSON.stringify(exportGraphSON(db, exportOpts), null, 2);
+          break;
+        case 'neo4j': {
+          const csv = exportNeo4jCSV(db, exportOpts);
+          if (opts.output) {
+            const base = opts.output.replace(/\.[^.]+$/, '') || opts.output;
+            fs.writeFileSync(`${base}-nodes.csv`, csv.nodes, 'utf-8');
+            fs.writeFileSync(`${base}-relationships.csv`, csv.relationships, 'utf-8');
+            console.log(`Exported to ${base}-nodes.csv and ${base}-relationships.csv`);
+          } else {
+            output = `--- nodes.csv ---\n${csv.nodes}\n\n--- relationships.csv ---\n${csv.relationships}`;
+          }
+          break;
         }
-        output = `--- nodes.csv ---\n${csv.nodes}\n\n--- relationships.csv ---\n${csv.relationships}`;
-        break;
+        default:
+          output = exportDOT(db, exportOpts);
+          break;
       }
-      default:
-        output = exportDOT(db, exportOpts);
-        break;
+    } finally {
+      close();
     }
 
-    db.close();
+    if (output === undefined) return;
 
     if (opts.output) {
       fs.writeFileSync(opts.output, output, 'utf-8');

package/src/cli/commands/exports.js

@@ -1,4 +1,4 @@
-import { fileExports } from '../../queries-cli.js';
+import { fileExports } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'exports <file>',
@@ -7,12 +7,8 @@ export const command = {
   options: [['--unused', 'Show only exports with zero consumers (dead exports)']],
   execute([file], opts, ctx) {
     fileExports(file, opts.db, {
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
       unused: opts.unused || false,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/flow.js

@@ -1,4 +1,4 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
   name: 'flow [name]',
@@ -20,17 +20,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { flow } = await import('../../commands/flow.js');
+    const { flow } = await import('../../presentation/flow.js');
     flow(name, opts.db, {
       list: opts.list,
       depth: parseInt(opts.depth, 10),
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/fn-impact.js

@@ -1,5 +1,5 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { fnImpact } from '../../queries-cli.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { fnImpact } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'fn-impact <name>',
@@ -20,11 +20,7 @@ export const command = {
       depth: parseInt(opts.depth, 10),
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/impact.js

@@ -1,4 +1,4 @@
-import { impactAnalysis } from '../../queries-cli.js';
+import { impactAnalysis } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'impact <file>',
@@ -6,11 +6,7 @@ export const command = {
   queryOpts: true,
   execute([file], opts, ctx) {
     impactAnalysis(file, opts.db, {
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/info.js

@@ -3,9 +3,9 @@ export const command = {
   description: 'Show codegraph engine info and diagnostics',
   async execute(_args, _opts, ctx) {
     const { getNativePackageVersion, isNativeAvailable, loadNative } = await import(
-      '../../native.js'
+      '../../infrastructure/native.js'
     );
-    const { getActiveEngine } = await import('../../parser.js');
+    const { getActiveEngine } = await import('../../domain/parser.js');
 
     const engine = ctx.program.opts().engine;
     const { name: activeName, version: activeVersion } = getActiveEngine({ engine });

package/src/cli/commands/map.js

@@ -1,4 +1,4 @@
-import { moduleMap } from '../../queries-cli.js';
+import { moduleMap } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'map',

package/src/cli/commands/mcp.js

@@ -7,7 +7,7 @@ export const command = {
     ['--repos <names>', 'Comma-separated list of allowed repo names (restricts access)'],
   ],
   async execute(_args, opts) {
-    const { startMCPServer } = await import('../../mcp.js');
+    const { startMCPServer } = await import('../../mcp/index.js');
     const mcpOpts = {};
     mcpOpts.multiRepo = opts.multiRepo || !!opts.repos;
     if (opts.repos) {

package/src/cli/commands/models.js

@@ -1,4 +1,4 @@
-import { DEFAULT_MODEL, MODELS } from '../../embeddings/index.js';
+import { DEFAULT_MODEL, MODELS } from '../../domain/search/index.js';
 
 export const command = {
   name: 'models',

package/src/cli/commands/owners.js

@@ -12,7 +12,7 @@ export const command = {
     ['-j, --json', 'Output as JSON'],
   ],
   async execute([target], opts, ctx) {
-    const { owners } = await import('../../commands/owners.js');
+    const { owners } = await import('../../presentation/owners.js');
     owners(opts.db, {
       owner: opts.owner,
       boundary: opts.boundary,

package/src/cli/commands/path.js

@@ -1,5 +1,5 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { symbolPath } from '../../queries-cli.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { symbolPath } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'path <from> <to>',

package/src/cli/commands/plot.js

@@ -1,6 +1,6 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { openReadonlyOrFail } from '../../db.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'plot',
@@ -22,43 +22,52 @@ export const command = {
     ['--color-by <mode>', 'Color nodes by: kind | role | community | complexity'],
   ],
   async execute(_args, opts, ctx) {
-    const { generatePlotHTML, loadPlotConfig } = await import('../../viewer.js');
+    const { generatePlotHTML, loadPlotConfig } = await import('../../features/graph-enrichment.js');
     const os = await import('node:os');
-    const db = openReadonlyOrFail(opts.db);
+    const { db, close } = openGraph(opts);
 
     let plotCfg;
-    if (opts.config) {
-      try {
-        plotCfg = JSON.parse(fs.readFileSync(opts.config, 'utf-8'));
-      } catch (e) {
-        console.error(`Failed to load config: ${e.message}`);
-        db.close();
-        process.exitCode = 1;
-        return;
+    let html;
+    try {
+      if (opts.config) {
+        try {
+          plotCfg = JSON.parse(fs.readFileSync(opts.config, 'utf-8'));
+        } catch (e) {
+          console.error(`Failed to load config: ${e.message}`);
+          process.exitCode = 1;
+          return;
+        }
+      } else {
+        plotCfg = loadPlotConfig(process.cwd());
+      }
+
+      if (opts.cluster) plotCfg.clusterBy = opts.cluster;
+      if (opts.colorBy) plotCfg.colorBy = opts.colorBy;
+      if (opts.sizeBy) plotCfg.sizeBy = opts.sizeBy;
+      if (opts.seed) plotCfg.seedStrategy = opts.seed;
+      if (opts.seedCount) plotCfg.seedCount = parseInt(opts.seedCount, 10);
+      if (opts.overlay) {
+        const parts = opts.overlay.split(',').map((s) => s.trim());
+        if (!plotCfg.overlays) plotCfg.overlays = {};
+        if (parts.includes('complexity')) plotCfg.overlays.complexity = true;
+        if (parts.includes('risk')) plotCfg.overlays.risk = true;
       }
-    } else {
-      plotCfg = loadPlotConfig(process.cwd());
-    }
 
-    if (opts.cluster) plotCfg.clusterBy = opts.cluster;
-    if (opts.colorBy) plotCfg.colorBy = opts.colorBy;
-    if (opts.sizeBy) plotCfg.sizeBy = opts.sizeBy;
-    if (opts.seed) plotCfg.seedStrategy = opts.seed;
-    if (opts.seedCount) plotCfg.seedCount = parseInt(opts.seedCount, 10);
-    if (opts.overlay) {
-      const parts = opts.overlay.split(',').map((s) => s.trim());
-      if (!plotCfg.overlays) plotCfg.overlays = {};
-      if (parts.includes('complexity')) plotCfg.overlays.complexity = true;
-      if (parts.includes('risk')) plotCfg.overlays.risk = true;
+      html = generatePlotHTML(db, {
+        fileLevel: !opts.functions,
+        noTests: ctx.resolveNoTests(opts),
+        minConfidence: parseFloat(opts.minConfidence),
+        config: plotCfg,
+      });
+    } finally {
+      close();
     }
 
-    const html = generatePlotHTML(db, {
-      fileLevel: !opts.functions,
-      noTests: ctx.resolveNoTests(opts),
-      minConfidence: parseFloat(opts.minConfidence),
-      config: plotCfg,
-    });
-    db.close();
+    if (!html) {
+      console.error('generatePlotHTML returned no output');
+      process.exitCode = 1;
+      return;
+    }
 
     const outPath = opts.output || path.join(os.tmpdir(), `codegraph-plot-${Date.now()}.html`);
     fs.writeFileSync(outPath, html, 'utf-8');

package/src/cli/commands/query.js

@@ -1,5 +1,5 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { fnDeps, symbolPath } from '../../queries-cli.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { fnDeps, symbolPath } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'query <name>',
@@ -38,11 +38,7 @@ export const command = {
         depth: parseInt(opts.depth, 10),
         file: opts.file,
         kind: opts.kind,
-        noTests: ctx.resolveNoTests(opts),
-        json: opts.json,
-        limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        ndjson: opts.ndjson,
+        ...ctx.resolveQueryOpts(opts),
       });
     }
   },

package/src/cli/commands/registry.js

@@ -1,13 +1,13 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { ConfigError } from '../../errors.js';
 import {
   listRepos,
   pruneRegistry,
   REGISTRY_PATH,
   registerRepo,
   unregisterRepo,
-} from '../../registry.js';
+} from '../../infrastructure/registry.js';
+import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
   name: 'registry',

package/src/cli/commands/roles.js

@@ -1,5 +1,5 @@
-import { VALID_ROLES } from '../../queries.js';
-import { roles } from '../../queries-cli.js';
+import { VALID_ROLES } from '../../domain/queries.js';
+import { roles } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'roles',
@@ -24,11 +24,7 @@ export const command = {
     roles(opts.db, {
       role: opts.role,
       file: opts.file,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/search.js

@@ -1,4 +1,4 @@
-import { search } from '../../embeddings/index.js';
+import { search } from '../../domain/search/index.js';
 
 export const command = {
   name: 'search <query>',

package/src/cli/commands/sequence.js

@@ -1,4 +1,4 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
   name: 'sequence <name>',
@@ -16,17 +16,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { sequence } = await import('../../commands/sequence.js');
+    const { sequence } = await import('../../presentation/sequence.js');
     sequence(name, opts.db, {
       depth: parseInt(opts.depth, 10),
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
       dataflow: opts.dataflow,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/snapshot.js

@@ -1,4 +1,9 @@
-import { snapshotDelete, snapshotList, snapshotRestore, snapshotSave } from '../../snapshot.js';
+import {
+  snapshotDelete,
+  snapshotList,
+  snapshotRestore,
+  snapshotSave,
+} from '../../features/snapshot.js';
 
 export const command = {
   name: 'snapshot',

package/src/cli/commands/stats.js

@@ -1,4 +1,4 @@
-import { stats } from '../../queries-cli.js';
+import { stats } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'stats',

package/src/cli/commands/structure.js

@@ -15,15 +15,16 @@ export const command = {
     ['--ndjson', 'Newline-delimited JSON output'],
   ],
   async execute([dir], opts, ctx) {
-    const { structureData, formatStructure } = await import('../../commands/structure.js');
+    const { structureData, formatStructure } = await import('../../presentation/structure.js');
+    const qOpts = ctx.resolveQueryOpts(opts);
     const data = structureData(opts.db, {
       directory: dir,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
       sort: opts.sort,
       full: opts.full,
-      noTests: ctx.resolveNoTests(opts),
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      noTests: qOpts.noTests,
+      limit: qOpts.limit,
+      offset: qOpts.offset,
     });
     if (!ctx.outputResult(data, 'directories', opts)) {
       console.log(formatStructure(data));

package/src/cli/commands/triage.js

@@ -1,5 +1,5 @@
-import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../queries.js';
+import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../domain/queries.js';
+import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
   name: 'triage',
@@ -31,7 +31,7 @@ export const command = {
   ],
   async execute(_args, opts, ctx) {
     if (opts.level === 'file' || opts.level === 'directory') {
-      const { hotspotsData, formatHotspots } = await import('../../commands/structure.js');
+      const { hotspotsData, formatHotspots } = await import('../../presentation/structure.js');
       const metric = opts.sort === 'risk' ? 'fan-in' : opts.sort;
       const data = hotspotsData(opts.db, {
         metric,
@@ -60,7 +60,7 @@ export const command = {
         throw new ConfigError('Invalid --weights JSON', { cause: err });
       }
     }
-    const { triage } = await import('../../commands/triage.js');
+    const { triage } = await import('../../presentation/triage.js');
     triage(opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,

package/src/cli/commands/watch.js

@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { watchProject } from '../../watcher.js';
+import { watchProject } from '../../domain/graph/watcher.js';
 
 export const command = {
   name: 'watch [dir]',

package/src/cli/commands/where.js

@@ -1,4 +1,4 @@
-import { where } from '../../queries-cli.js';
+import { where } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'where [name]',
@@ -14,11 +14,7 @@ export const command = {
     const target = opts.file || name;
     where(target, opts.db, {
       file: !!opts.file,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/index.js

@@ -2,10 +2,16 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { pathToFileURL } from 'node:url';
 import { Command } from 'commander';
-import { ConfigError } from '../errors.js';
-import { setVerbose } from '../logger.js';
-import { checkForUpdates, printUpdateNotification } from '../update-check.js';
-import { applyQueryOpts, config, formatSize, resolveNoTests } from './shared/options.js';
+import { setVerbose } from '../infrastructure/logger.js';
+import { checkForUpdates, printUpdateNotification } from '../infrastructure/update-check.js';
+import { ConfigError } from '../shared/errors.js';
+import {
+  applyQueryOpts,
+  config,
+  formatSize,
+  resolveNoTests,
+  resolveQueryOpts,
+} from './shared/options.js';
 import { outputResult } from './shared/output.js';
 
 const __cliDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
@@ -35,7 +41,7 @@ program
   });
 
 /** Shared context passed to every command's execute(). */
-const ctx = { config, resolveNoTests, formatSize, outputResult, program };
+const ctx = { config, resolveNoTests, resolveQueryOpts, formatSize, outputResult, program };
 
 /**
  * Register a command definition onto a Commander parent.

package/src/cli/shared/open-graph.js

@@ -0,0 +1,13 @@
+import { openReadonlyOrFail } from '../../db/index.js';
+
+/**
+ * Open the graph database in readonly mode with a clean close() handle.
+ *
+ * @param {object} [opts]
+ * @param {string} [opts.db] - Custom path to graph.db
+ * @returns {{ db: import('better-sqlite3').Database, close: () => void }}
+ */
+export function openGraph(opts = {}) {
+  const db = openReadonlyOrFail(opts.db);
+  return { db, close: () => db.close() };
+}