@codeyam/codeyam-cli 0.1.0-staging.dd216e0 → 0.1.0-staging.e090cb3

package/codeyam-cli/src/commands/wipe.js

@@ -0,0 +1,108 @@
+import * as fs from 'fs';
+import * as path from 'path';
+import * as readline from 'readline';
+import { error, header, info, ProgressReporter, success, warn, withoutSpinner, } from "../utils/progress.js";
+import { testEnvironment, requireBranchAndProject } from "../utils/database.js";
+import { getWipeStats, wipeProject, formatWipeStats, hasDataToWipe, } from "../utils/wipe.js";
+import { getProjectRoot } from "../state.js";
+/**
+ * Prompt user for confirmation.
+ */
+async function confirm(message) {
+    const rl = readline.createInterface({
+        input: process.stdin,
+        output: process.stdout,
+    });
+    return new Promise((resolve) => {
+        rl.question(`${message} [y/N] `, (answer) => {
+            rl.close();
+            resolve(answer.toLowerCase() === 'y' || answer.toLowerCase() === 'yes');
+        });
+    });
+}
+const wipeCommand = {
+    command: 'wipe',
+    describe: 'Delete all analysis data for this project (entities, analyses, scenarios)',
+    builder: {
+        yes: {
+            type: 'boolean',
+            alias: 'y',
+            describe: 'Skip confirmation prompt',
+            default: false,
+        },
+    },
+    handler: async (argv) => {
+        header('CodeYam Wipe');
+        const progress = new ProgressReporter();
+        // Find project root directory
+        const projectRoot = getProjectRoot();
+        if (!projectRoot) {
+            error('Not in a CodeYam project. Run: codeyam init');
+            return;
+        }
+        const configPath = path.join(projectRoot, '.codeyam', 'config.json');
+        try {
+            // Load project configuration
+            progress.start('Loading project configuration...');
+            const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+            const { projectSlug } = config;
+            if (!projectSlug) {
+                progress.fail('Invalid project configuration');
+                error('Missing project slug. Try reinitializing with: codeyam init --force');
+                return;
+            }
+            progress.succeed('Loaded project configuration');
+            // Test database connection
+            progress.start('Validating environment...');
+            const connectionOk = await withoutSpinner(() => testEnvironment());
+            if (!connectionOk) {
+                progress.fail('Environment validation failed');
+                return;
+            }
+            progress.succeed('Environment validated');
+            // Load project
+            progress.start('Loading project...');
+            const { project } = await requireBranchAndProject(projectSlug);
+            progress.succeed('Project loaded');
+            // Get wipe stats
+            progress.start('Counting records...');
+            const stats = await getWipeStats(project.id);
+            progress.succeed('Record count complete');
+            // Check if there's anything to wipe
+            if (!hasDataToWipe(stats)) {
+                console.log();
+                success('Nothing to wipe');
+                info('Project has no analysis data');
+                return;
+            }
+            // Show what will be deleted
+            console.log();
+            warn('⚠️  This will permanently delete:');
+            console.log(formatWipeStats(stats));
+            console.log();
+            // Confirm unless --yes flag is set
+            if (!argv.yes) {
+                const confirmed = await confirm('Continue?');
+                if (!confirmed) {
+                    info('Wipe cancelled');
+                    return;
+                }
+            }
+            console.log();
+            // Execute wipe
+            progress.start('Wiping project data...');
+            await wipeProject(project.id);
+            progress.succeed('Project data wiped');
+            console.log();
+            success('Wipe completed successfully');
+            info('Run "codeyam baseline" to create a new baseline analysis');
+        }
+        catch (err) {
+            progress.fail('Wipe failed');
+            error(err.message);
+            process.exit(1);
+        }
+    },
+};
+export default wipeCommand;
+//# sourceMappingURL=wipe.js.map

package/codeyam-cli/src/commands/wipe.js.map

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package/codeyam-cli/src/utils/__tests__/serverVersionStaleness.test.js

@@ -0,0 +1,81 @@
+/**
+ * Tests for server version staleness detection.
+ *
+ * These tests verify the logic used in backgroundServer.ts for detecting
+ * when a running server has a different CLI version than the current CLI.
+ *
+ * Note: backgroundServer.ts cannot be directly imported in tests due to
+ * import.meta.url usage, so we test the logic pattern directly.
+ */
+describe('Server Version Staleness', () => {
+    /**
+     * Simulates the version mismatch detection logic from backgroundServer.ts:
+     *
+     * if (state.cliVersion !== cliVersion) {
+     *   // restart needed
+     * }
+     */
+    function shouldRestartServer(serverVersion, currentCliVersion) {
+        return serverVersion !== currentCliVersion;
+    }
+    describe('version mismatch detection', () => {
+        it('should detect version mismatch and trigger restart', () => {
+            const serverVersion = '1.0.0';
+            const currentCliVersion = '2.0.0';
+            expect(shouldRestartServer(serverVersion, currentCliVersion)).toBe(true);
+        });
+        it('should reuse server when versions match', () => {
+            const serverVersion = '2.0.0';
+            const currentCliVersion = '2.0.0';
+            expect(shouldRestartServer(serverVersion, currentCliVersion)).toBe(false);
+        });
+        it('should restart server when state has no cliVersion (backwards compat)', () => {
+            const serverVersion = undefined; // Old state file format
+            const currentCliVersion = '2.0.0';
+            // undefined !== '2.0.0' should be true, triggering restart
+            expect(shouldRestartServer(serverVersion, currentCliVersion)).toBe(true);
+        });
+        it('should handle patch version differences', () => {
+            expect(shouldRestartServer('1.0.0', '1.0.1')).toBe(true);
+            expect(shouldRestartServer('1.0.1', '1.0.0')).toBe(true);
+        });
+        it('should handle minor version differences', () => {
+            expect(shouldRestartServer('1.0.0', '1.1.0')).toBe(true);
+            expect(shouldRestartServer('1.1.0', '1.0.0')).toBe(true);
+        });
+        it('should handle major version differences', () => {
+            expect(shouldRestartServer('1.0.0', '2.0.0')).toBe(true);
+            expect(shouldRestartServer('2.0.0', '1.0.0')).toBe(true);
+        });
+        it('should handle pre-release versions', () => {
+            expect(shouldRestartServer('1.0.0-beta.1', '1.0.0')).toBe(true);
+            expect(shouldRestartServer('1.0.0', '1.0.0-beta.1')).toBe(true);
+            expect(shouldRestartServer('1.0.0-beta.1', '1.0.0-beta.1')).toBe(false);
+        });
+    });
+    describe('ServerState cliVersion field', () => {
+        it('should allow ServerState without cliVersion for backwards compat', () => {
+            const oldState = {
+                pid: 1234,
+                port: 3111,
+                url: 'http://localhost:3111',
+                startTime: Date.now(),
+                projectRoot: '/test/project',
+                // No cliVersion - old format
+            };
+            expect(oldState.cliVersion).toBeUndefined();
+        });
+        it('should include cliVersion in new ServerState', () => {
+            const newState = {
+                pid: 1234,
+                port: 3111,
+                url: 'http://localhost:3111',
+                startTime: Date.now(),
+                projectRoot: '/test/project',
+                cliVersion: '2.0.0',
+            };
+            expect(newState.cliVersion).toBe('2.0.0');
+        });
+    });
+});
+//# sourceMappingURL=serverVersionStaleness.test.js.map

package/codeyam-cli/src/utils/__tests__/serverVersionStaleness.test.js.map

@@ -0,0 +1 @@
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package/codeyam-cli/src/utils/__tests__/setupClaudeCodeSettings.test.js

@@ -6,6 +6,28 @@ jest.mock('fs');
 jest.mock('path');
 const mockFs = fs;
 const mockPath = path;
+// Shared permission lists for assertions
+const memoryPermissions = [
+    'Skill(codeyam-memory)',
+    'Skill(codeyam-new-rule)',
+    'Bash(codeyam)',
+    'Bash(codeyam:*)',
+    'Read(.codeyam/**)',
+    'Edit(.codeyam/**)',
+    'Write(.codeyam/**)',
+    'Glob(.codeyam/**)',
+];
+const simulationPermissions = [
+    'Skill(codeyam-setup)',
+    'Skill(codeyam-sim)',
+    'Skill(codeyam-debug)',
+    'Skill(codeyam-test)',
+    'Skill(codeyam-verify)',
+    'Read(/tmp/codeyam/**)',
+    'Edit(/tmp/codeyam/**)',
+    'Write(/tmp/codeyam/**)',
+    'Glob(/tmp/codeyam/**)',
+];
 describe('setupClaudeCodeSettings', () => {
     const projectRoot = '/Users/testuser/myproject';
     const claudeDir = '/Users/testuser/myproject/.claude';
@@ -23,10 +45,8 @@ describe('setupClaudeCodeSettings', () => {
     describe('directory and file creation', () => {
         test('creates .claude directory if it does not exist', () => {
             mockFs.existsSync.mockImplementation((p) => {
-                // .claude directory doesn't exist
                 if (p === claudeDir)
                     return false;
-                // settings.local.json doesn't exist either
                 if (p === settingsPath)
                     return false;
                 return false;
@@ -39,12 +59,10 @@ describe('setupClaudeCodeSettings', () => {
             });
             expect(result).toBe(true);
         });
-        test('creates new settings file with all CodeYam permissions', () => {
+        test('creates new settings file with only memory permissions by default', () => {
             mockFs.existsSync.mockImplementation((p) => {
-                // .claude directory exists
                 if (p === claudeDir)
                     return true;
-                // settings.local.json doesn't exist yet
                 if (p === settingsPath)
                     return false;
                 return false;
@@ -52,90 +70,73 @@ describe('setupClaudeCodeSettings', () => {
             mockFs.writeFileSync.mockImplementation(() => undefined);
             const result = setupClaudeCodeSettings(projectRoot);
             expect(mockFs.writeFileSync).toHaveBeenCalledWith(settingsPath, expect.any(String), 'utf8');
-            // Parse the written content to verify structure
             const writtenContent = mockFs.writeFileSync.mock
                 .calls[0][1];
             const settings = JSON.parse(writtenContent);
-            expect(settings.permissions.allow).toContain('Skill(codeyam-setup)');
-            expect(settings.permissions.allow).toContain('Bash(codeyam)');
-            expect(settings.permissions.allow).toContain('Read(.codeyam/**)');
+            // Should include memory permissions
+            for (const perm of memoryPermissions) {
+                expect(settings.permissions.allow).toContain(perm);
+            }
+            // Should NOT include simulation permissions
+            for (const perm of simulationPermissions) {
+                expect(settings.permissions.allow).not.toContain(perm);
+            }
             expect(result).toBe(true);
         });
     });
-    describe('adding permissions to existing settings', () => {
-        test('adds CodeYam permissions to existing settings without allow list', () => {
+    describe('memory mode (default)', () => {
+        test('adds only memory permissions when mode is memory', () => {
             mockFs.existsSync.mockReturnValue(true);
             mockFs.readFileSync.mockReturnValue(JSON.stringify({ otherSetting: 'value' }));
             let writtenSettings;
             mockFs.writeFileSync.mockImplementation((_path, content) => {
                 writtenSettings = JSON.parse(content);
             });
-            const result = setupClaudeCodeSettings(projectRoot);
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-setup)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-sim)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-debug)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-test)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-verify)');
-            expect(writtenSettings.permissions.allow).toContain('Bash(codeyam:*)');
+            const result = setupClaudeCodeSettings(projectRoot, { mode: 'memory' });
+            for (const perm of memoryPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            for (const perm of simulationPermissions) {
+                expect(writtenSettings.permissions.allow).not.toContain(perm);
+            }
             expect(writtenSettings.otherSetting).toBe('value');
             expect(result).toBe(true);
         });
-        test('adds CodeYam permissions to existing allow list', () => {
+        test('default mode (no options) behaves as memory mode', () => {
             mockFs.existsSync.mockReturnValue(true);
-            mockFs.readFileSync.mockReturnValue(JSON.stringify({
-                permissions: {
-                    allow: ['some-other-tool'],
-                },
-            }));
+            mockFs.readFileSync.mockReturnValue(JSON.stringify({}));
             let writtenSettings;
             mockFs.writeFileSync.mockImplementation((_path, content) => {
                 writtenSettings = JSON.parse(content);
             });
-            const result = setupClaudeCodeSettings(projectRoot);
-            expect(writtenSettings.permissions.allow).toContain('some-other-tool');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-setup)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-sim)');
-            expect(writtenSettings.permissions.allow).toContain('Write(.codeyam/**)');
-            expect(result).toBe(true);
+            setupClaudeCodeSettings(projectRoot);
+            for (const perm of memoryPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            for (const perm of simulationPermissions) {
+                expect(writtenSettings.permissions.allow).not.toContain(perm);
+            }
         });
-        test('does not duplicate CodeYam permissions if already present', () => {
+        test('does not duplicate memory permissions if already present', () => {
             mockFs.existsSync.mockReturnValue(true);
             mockFs.readFileSync.mockReturnValue(JSON.stringify({
                 permissions: {
-                    allow: [
-                        'Skill(codeyam-setup)',
-                        'Skill(codeyam-sim)',
-                        'Skill(codeyam-debug)',
-                        'Skill(codeyam-test)',
-                        'Skill(codeyam-verify)',
-                        'Bash(codeyam)',
-                        'Bash(codeyam:*)',
-                        'Read(.codeyam/**)',
-                        'Edit(.codeyam/**)',
-                        'Write(.codeyam/**)',
-                        'Glob(.codeyam/**)',
-                        'Read(/tmp/codeyam/**)',
-                        'Edit(/tmp/codeyam/**)',
-                        'Write(/tmp/codeyam/**)',
-                        'Glob(/tmp/codeyam/**)',
-                        'other-tool',
-                    ],
+                    allow: [...memoryPermissions, 'other-tool'],
                 },
             }));
             const result = setupClaudeCodeSettings(projectRoot);
-            // Should not write if all permissions are already present
+            // Should not write if all memory permissions are already present
             expect(mockFs.writeFileSync).not.toHaveBeenCalled();
             expect(result).toBe(true);
         });
-        test('adds only missing CodeYam permissions', () => {
+        test('adds only missing memory permissions', () => {
             mockFs.existsSync.mockReturnValue(true);
             mockFs.readFileSync.mockReturnValue(JSON.stringify({
                 permissions: {
                     allow: [
-                        'Skill(codeyam-setup)',
-                        'Skill(codeyam-sim)',
+                        'Skill(codeyam-memory)',
                         'other-tool',
-                        // Missing: Skill(codeyam-debug), Skill(codeyam-test), Skill(codeyam-verify), all Bash and file ops
+                        // Missing: Skill(codeyam-new-rule), Bash, file ops
                     ],
                 },
             }));
@@ -144,20 +145,71 @@ describe('setupClaudeCodeSettings', () => {
                 writtenSettings = JSON.parse(content);
             });
             const result = setupClaudeCodeSettings(projectRoot);
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-setup)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-sim)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-debug)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-test)');
-            expect(writtenSettings.permissions.allow).toContain('Skill(codeyam-verify)');
-            expect(writtenSettings.permissions.allow).toContain('Bash(codeyam)');
+            for (const perm of memoryPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
             expect(writtenSettings.permissions.allow).toContain('other-tool');
             // Should not duplicate existing ones
-            const setupCount = writtenSettings.permissions.allow.filter((p) => p === 'Skill(codeyam-setup)').length;
-            expect(setupCount).toBe(1);
+            const memoryCount = writtenSettings.permissions.allow.filter((p) => p === 'Skill(codeyam-memory)').length;
+            expect(memoryCount).toBe(1);
+            expect(result).toBe(true);
+        });
+    });
+    describe('full mode', () => {
+        test('adds all permissions (memory + simulation) in full mode', () => {
+            mockFs.existsSync.mockReturnValue(true);
+            mockFs.readFileSync.mockReturnValue(JSON.stringify({ otherSetting: 'value' }));
+            let writtenSettings;
+            mockFs.writeFileSync.mockImplementation((_path, content) => {
+                writtenSettings = JSON.parse(content);
+            });
+            const result = setupClaudeCodeSettings(projectRoot, { mode: 'full' });
+            for (const perm of memoryPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            for (const perm of simulationPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            expect(writtenSettings.otherSetting).toBe('value');
+            expect(result).toBe(true);
+        });
+        test('does not duplicate full permissions if already present', () => {
+            const allPermissions = [...memoryPermissions, ...simulationPermissions];
+            mockFs.existsSync.mockReturnValue(true);
+            mockFs.readFileSync.mockReturnValue(JSON.stringify({
+                permissions: {
+                    allow: [...allPermissions, 'other-tool'],
+                },
+            }));
+            const result = setupClaudeCodeSettings(projectRoot, { mode: 'full' });
+            expect(mockFs.writeFileSync).not.toHaveBeenCalled();
+            expect(result).toBe(true);
+        });
+        test('adds simulation permissions to existing memory-only settings', () => {
+            mockFs.existsSync.mockReturnValue(true);
+            mockFs.readFileSync.mockReturnValue(JSON.stringify({
+                permissions: {
+                    allow: [...memoryPermissions, 'other-tool'],
+                },
+            }));
+            let writtenSettings;
+            mockFs.writeFileSync.mockImplementation((_path, content) => {
+                writtenSettings = JSON.parse(content);
+            });
+            const result = setupClaudeCodeSettings(projectRoot, { mode: 'full' });
+            for (const perm of memoryPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            for (const perm of simulationPermissions) {
+                expect(writtenSettings.permissions.allow).toContain(perm);
+            }
+            expect(writtenSettings.permissions.allow).toContain('other-tool');
+            // No duplicates
+            const memoryCount = writtenSettings.permissions.allow.filter((p) => p === 'Skill(codeyam-memory)').length;
+            expect(memoryCount).toBe(1);
             expect(result).toBe(true);
         });
     });
-    // Note: Stop hook configuration tests removed - hook functionality is currently disabled
     describe('error handling', () => {
         test('handles malformed JSON gracefully and creates new settings', () => {
             mockFs.existsSync.mockReturnValue(true);
@@ -190,31 +242,25 @@ describe('setupClaudeCodeSettings', () => {
         });
     });
     describe('idempotency', () => {
-        test('returns true when settings are already fully configured', () => {
+        test('returns true without writing when memory settings are fully configured', () => {
             mockFs.existsSync.mockReturnValue(true);
             mockFs.readFileSync.mockReturnValue(JSON.stringify({
                 permissions: {
-                    allow: [
-                        'Skill(codeyam-setup)',
-                        'Skill(codeyam-sim)',
-                        'Skill(codeyam-debug)',
-                        'Skill(codeyam-test)',
-                        'Skill(codeyam-verify)',
-                        'Bash(codeyam)',
-                        'Bash(codeyam:*)',
-                        'Read(.codeyam/**)',
-                        'Edit(.codeyam/**)',
-                        'Write(.codeyam/**)',
-                        'Glob(.codeyam/**)',
-                        'Read(/tmp/codeyam/**)',
-                        'Edit(/tmp/codeyam/**)',
-                        'Write(/tmp/codeyam/**)',
-                        'Glob(/tmp/codeyam/**)',
-                    ],
+                    allow: [...memoryPermissions],
                 },
             }));
             const result = setupClaudeCodeSettings(projectRoot);
-            // Should not write if already configured
+            expect(mockFs.writeFileSync).not.toHaveBeenCalled();
+            expect(result).toBe(true);
+        });
+        test('returns true without writing when full settings are fully configured', () => {
+            mockFs.existsSync.mockReturnValue(true);
+            mockFs.readFileSync.mockReturnValue(JSON.stringify({
+                permissions: {
+                    allow: [...memoryPermissions, ...simulationPermissions],
+                },
+            }));
+            const result = setupClaudeCodeSettings(projectRoot, { mode: 'full' });
             expect(mockFs.writeFileSync).not.toHaveBeenCalled();
             expect(result).toBe(true);
         });

package/codeyam-cli/src/utils/__tests__/setupClaudeCodeSettings.test.js.map

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package/codeyam-cli/src/utils/analysisRunner.js

@@ -3,7 +3,6 @@ import * as path from 'path';
 import { ProgressReporter, withoutSpinner } from "./progress.js";
 import { createFakeCommit, requireBranchAndProject, testEnvironment, } from "./database.js";
 import { startBackgroundServer } from "./backgroundServer.js";
-import { isServerRunning } from "./serverState.js";
 import { updateCommitMetadata } from "../../../packages/database/index.js";
 import { getCurrentEntities } from "../webserver/app/lib/database.js";
 import { pushNewCommitRun } from "../../../packages/utils/server.js";
@@ -49,27 +48,25 @@ export async function runAnalysisForEntities(options) {
     reporter.start('Loading project from database...');
     const { project, branch } = await requireBranchAndProject(projectSlug);
     reporter.succeed('Loaded project and branch');
-    // Start web server if not already running
+    // Start web server if not already running (also handles version mismatch detection)
     reporter.start('Starting web server...');
-    const { running, state } = isServerRunning();
-    let serverUrl;
-    if (running && state) {
-        serverUrl = state.url;
+    const { url: serverUrl, wasAlreadyRunning } = await startBackgroundServer({
+        port: 3111,
+        rootPath: projectRoot,
+        project,
+        branch,
+    });
+    if (wasAlreadyRunning) {
         reporter.succeed(`Web server already running at ${serverUrl}`);
     }
     else {
-        const { url } = await startBackgroundServer({
-            port: 3111,
-            rootPath: projectRoot,
-            project,
-            branch,
-        });
-        serverUrl = url;
         reporter.succeed(`Web server started at ${serverUrl}`);
     }
-    // Resolve entity SHAs if entity names are provided
+    // Look up entities in the specified file paths
+    // This ensures entityShas is populated for Historic Activity tracking
     let entityShas = [];
     if (entityNames && entityNames.length > 0) {
+        // Specific entity names provided - look up by name
         reporter.start(`Looking up ${entityNames.length} entities...`);
         const entities = await getCurrentEntities({
             projectId: project.id,
@@ -83,6 +80,23 @@ export async function runAnalysisForEntities(options) {
         entityShas = entities.map((e) => e.sha);
         reporter.succeed(`Found ${entities.length} entities`);
     }
+    else {
+        // No specific entity names - look up all entities in the file paths
+        reporter.start(`Looking up entities in ${filePaths.length} files...`);
+        const entities = await getCurrentEntities({
+            projectId: project.id,
+            filePaths,
+        });
+        if (entities.length > 0) {
+            entityShas = entities.map((e) => e.sha);
+            reporter.succeed(`Found ${entities.length} entities in files`);
+        }
+        else {
+            // No existing entities found - this is fine for new files
+            // The analyzer will discover and create entities
+            reporter.succeed(`No existing entities found (will be discovered)`);
+        }
+    }
     // Create fake commit for analysis
     reporter.start('Creating analysis commit...');
     const fakeCommit = await createFakeCommit(project, branch, filePaths);
@@ -98,7 +112,7 @@ export async function runAnalysisForEntities(options) {
             capturesCompleted: 0,
             createdAt: new Date().toISOString(),
         },
-        updateCallback: (metadata, commit) => {
+        updateCallback: (metadata) => {
             const existingRun = metadata.currentRun;
             if (existingRun && existingRun.id && existingRun.archivedAt) {
                 return;