cli: git sync improvements v2 (#6220)

* log when override is applied vs default taken in git sync

* simplify cli merging options + add explicit override test

* gitsync-settings pull/push ask for confirmation or --yes if tty

* cli legacy backend repo setting detected + interactive migration

cli/conf.ts

@@ -108,31 +108,45 @@ export function getEffectiveSettings(
 ): SyncOptions {
   // Start with empty object - no defaults
   let effective = {} as SyncOptions;
-  
+
   // Merge top-level settings from config (which contains user's chosen defaults)
   Object.keys(config).forEach(key => {
     if (key !== 'overrides' && config[key as keyof SyncOptions] !== undefined) {
       (effective as any)[key] = config[key as keyof SyncOptions];
     }
   });
-  
+
   if (!config.overrides) {
+    if (repo) {
+      log.info(`No overrides found in wmill.yaml, using top-level settings (repository flag ignored)`);
+    }
     return effective;
   }
-  
+
   // Construct override keys using the single format
   const workspaceKey = `${baseUrl}:${workspaceId}:*`;
   const repoKey = `${baseUrl}:${workspaceId}:${repo}`;
-  
+
+  let appliedOverrides: string[] = [];
+
   // Apply workspace-level overrides
   if (config.overrides[workspaceKey]) {
     Object.assign(effective, config.overrides[workspaceKey]);
+    appliedOverrides.push("workspace-level");
   }
-  
+
   // Apply repository-specific overrides (overrides workspace-level)
   if (config.overrides[repoKey]) {
     Object.assign(effective, config.overrides[repoKey]);
+    appliedOverrides.push("repository-specific");
+  } else if (repo) {
+    // Repository was specified but no override found
+    log.info(`Repository override not found for "${repo}", using ${appliedOverrides.length > 0 ? appliedOverrides.join(" + ") : "top-level"} settings`);
   }
-  
+
+  if (appliedOverrides.length > 0) {
+    log.info(`Applied ${appliedOverrides.join(" + ")} overrides${repo ? ` for repository "${repo}"` : ""}`);
+  }
+
   return effective;
 }

cli/gitsync-settings.ts

@@ -1,4 +1,4 @@
-import { colors, Command, log, yamlStringify } from "./deps.ts";
+import { colors, Command, Confirm, log, yamlStringify } from "./deps.ts";
 import { GlobalOptions } from "./types.ts";
 import { requireLogin } from "./auth.ts";
 import { resolveWorkspace } from "./context.ts";
@@ -164,6 +164,147 @@ function includeTypeToSyncOptions(
   };
 }
 
+// Shared migration function for legacy repositories
+async function handleLegacyRepositoryMigration(
+  selectedRepo: any,
+  gitSyncSettings: any,
+  workspace: any,
+  opts: { yes?: boolean },
+  operationName: string = "operation"
+): Promise<any> {
+  if (selectedRepo.settings) {
+    return selectedRepo; // Already migrated
+  }
+
+  // This repository is in legacy format - handle migration
+  if (!gitSyncSettings.include_path || !gitSyncSettings.include_type) {
+    throw new Error(
+      `Repository "${selectedRepo.git_repo_resource_path}" has legacy format but workspace-level include_path or include_type is missing. This indicates corrupted git-sync settings.`
+    );
+  }
+
+  const workspaceIncludePath = gitSyncSettings.include_path;
+  const workspaceIncludeType = gitSyncSettings.include_type;
+
+  if (Deno.stdout.isTerminal() && !opts.yes) {
+    // Interactive mode - show migration prompt
+    console.log(colors.yellow('\n⚠️  Legacy git-sync settings detected!'));
+    console.log(`\nRepository "${selectedRepo.git_repo_resource_path}" has legacy settings format.`);
+    console.log('The new format allows per-repository filter configuration.');
+    if (operationName === "push") {
+      console.log('This repository must be migrated before pushing settings.\n');
+    } else {
+      console.log('\n');
+    }
+
+    console.log(colors.bold('Current workspace-level settings:'));
+    console.log(`  Include paths: ${workspaceIncludePath.join(', ')}`);
+    console.log(`  Include types: ${workspaceIncludeType.join(', ')}\n`);
+
+    // Show what the migration will do
+    let finalIncludeType = [...workspaceIncludeType];
+    if (selectedRepo.exclude_types_override && selectedRepo.exclude_types_override.length > 0) {
+      const originalCount = finalIncludeType.length;
+      finalIncludeType = finalIncludeType.filter(
+        type => !selectedRepo.exclude_types_override.includes(type)
+      );
+      const excludedCount = originalCount - finalIncludeType.length;
+      console.log(colors.yellow(`Repository excludes ${excludedCount} types: ${selectedRepo.exclude_types_override.join(', ')}`));
+    }
+
+    console.log(colors.bold('\nAfter migration, repository will have:'));
+    console.log(`  Include paths: ${workspaceIncludePath.join(', ')}`);
+    console.log(`  Include types: ${finalIncludeType.join(', ')}\n`);
+
+    const confirm = await Confirm.prompt({
+      message: operationName === "push"
+        ? 'Do you want to migrate this repository before pushing?'
+        : 'Do you want to migrate this repository?',
+      default: true
+    });
+
+    if (!confirm) {
+      const message = operationName === "push"
+        ? '\n⚠️  Migration skipped. Cannot push to legacy repository.'
+        : '\n⚠️  Migration skipped. You can migrate later via the UI.';
+      console.log(colors.yellow(message));
+      if (operationName === "push") {
+        return null; // Signal to exit push operation
+      }
+      throw new Error('Migration cancelled by user');
+    }
+
+    // Perform the migration
+    let migratedIncludeType = [...workspaceIncludeType];
+    if (selectedRepo.exclude_types_override && selectedRepo.exclude_types_override.length > 0) {
+      migratedIncludeType = migratedIncludeType.filter(
+        type => !selectedRepo.exclude_types_override.includes(type)
+      );
+    }
+
+    const migratedRepo = {
+      ...selectedRepo,
+      settings: {
+        include_path: [...workspaceIncludePath],
+        include_type: migratedIncludeType,
+        exclude_path: [],
+        extra_include_path: []
+      }
+    };
+
+    // Remove the old field
+    delete migratedRepo.exclude_types_override;
+
+    // Update the backend with migrated repository
+    const updatedRepositories = gitSyncSettings.repositories.map((repo: any) => {
+      if (repo.git_repo_resource_path === selectedRepo.git_repo_resource_path) {
+        return migratedRepo;
+      }
+      return repo;
+    });
+
+    await wmill.editWorkspaceGitSyncConfig({
+      workspace: workspace.workspaceId,
+      requestBody: {
+        git_sync_settings: {
+          repositories: updatedRepositories,
+          // Keep workspace-level settings if other repos are still legacy
+          ...(gitSyncSettings.repositories.some((r: any) => r.git_repo_resource_path !== selectedRepo.git_repo_resource_path && !r.settings) && {
+            include_path: workspaceIncludePath,
+            include_type: workspaceIncludeType
+          })
+        }
+      }
+    });
+
+    console.log(colors.green('\n✓ Repository migration completed successfully!'));
+    if (operationName === "push") {
+      console.log('Now proceeding with push operation...\n');
+    }
+    return migratedRepo;
+
+  } else {
+    // Non-interactive mode - show error
+    console.error(colors.red('\n❌ Legacy git-sync settings detected!'));
+    console.error(`\nRepository "${selectedRepo.git_repo_resource_path}" has legacy settings format.`);
+    if (operationName === "push") {
+      console.error('This repository must be migrated before pushing settings.');
+    }
+    console.error('Please choose one of the following options:\n');
+    console.error('1. Go to the Windmill UI > Workspace Settings > Git Sync');
+    console.error('   Review and save this repository to migrate to the new format.\n');
+    console.error('2. Run this command in interactive mode (with TTY) to migrate.');
+    console.error(`   Example: wmill gitsync-settings ${operationName}\n`);
+    if (operationName === "push") {
+      console.error('3. Pull settings first to migrate: wmill gitsync-settings pull\n');
+    } else {
+      console.error('3. Push local settings to override backend settings:');
+      console.error('   wmill gitsync-settings push\n');
+    }
+    Deno.exit(1);
+  }
+}
+
 // Convert SyncOptions boolean flags to backend include_type array
 function syncOptionsToIncludeType(opts: SyncOptions): string[] {
   const includeTypes: string[] = [];
@@ -279,6 +420,31 @@ function displayChanges(
   }
 }
 
+async function selectAndLogRepository(
+  repositories: GitSyncRepository[],
+  repository?: string,
+): Promise<GitSyncRepository> {
+  let selectedRepo: GitSyncRepository;
+
+  if (repository) {
+    const found = repositories.find(
+      (r: GitSyncRepository) =>
+        r.git_repo_resource_path === repository ||
+        r.git_repo_resource_path === `$res:${repository}`,
+    );
+    if (!found) {
+      throw new Error(`Repository ${repository} not found`);
+    }
+    selectedRepo = found;
+    const repoPath = selectedRepo.git_repo_resource_path.replace(/^\$res:/, "");
+    log.info(colors.cyan(`Using repository: ${colors.bold(repoPath)}`));
+  } else {
+    selectedRepo = await selectRepository(repositories);
+  }
+
+  return selectedRepo;
+}
+
 async function pullGitSyncSettings(
   opts: GlobalOptions & {
     repository?: string;
@@ -289,6 +455,7 @@ async function pullGitSyncSettings(
     replace?: boolean;
     override?: boolean;
     withBackendSettings?: string;
+    yes?: boolean;
   },
 ) {
   const workspace = await resolveWorkspace(opts);
@@ -401,22 +568,19 @@ async function pullGitSyncSettings(
     }
 
     // Find the repository to work with
-    let selectedRepo: GitSyncRepository;
-    if (opts.repository) {
-      const found = settings.git_sync.repositories.find(
-        (r: GitSyncRepository) =>
-          r.git_repo_resource_path === opts.repository ||
-          r.git_repo_resource_path === `$res:${opts.repository}`,
-      );
-      if (!found) {
-        throw new Error(`Repository ${opts.repository} not found`);
-      }
-      selectedRepo = found;
-    } else {
-      selectedRepo = await selectRepository(
-        settings.git_sync.repositories,
-      );
-    }
+    let selectedRepo = await selectAndLogRepository(
+      settings.git_sync.repositories,
+      opts.repository,
+    );
+
+    // Check if the selected repository needs migration and handle it
+    selectedRepo = await handleLegacyRepositoryMigration(
+      selectedRepo,
+      settings.git_sync,
+      workspace,
+      opts,
+      "pull"
+    );
 
     // Convert backend settings to SyncOptions format
     const backendSyncOptions: SyncOptions = {
@@ -534,7 +698,7 @@ async function pullGitSyncSettings(
         );
       } else {
         if (hasChanges) {
-          log.info("Changes that would be made:");
+          log.info("Changes that would be applied locally:");
           const changes = generateChanges(normalizedCurrent, normalizedBackend);
 
           if (Object.keys(changes).length === 0) {
@@ -573,7 +737,14 @@ async function pullGitSyncSettings(
       );
       const hasConflict = !deepEqual(gitSyncBackend, gitSyncCurrent);
 
-      if (hasConflict && Deno.stdin.isTerminal()) {
+      if (hasConflict && !opts.yes && Deno.stdin.isTerminal()) {
+        // Show the diff first
+        log.info("Changes that would be applied locally:");
+        const changes = generateChanges(currentSettings, backendSyncOptions);
+        if (Object.keys(changes).length > 0) {
+          displayChanges(changes);
+        }
+
         // Interactive mode - ask user
         const { Select } = await import("./deps.ts");
         const choice = await Select.prompt({
@@ -607,6 +778,16 @@ async function pullGitSyncSettings(
             repoPath,
           );
         }
+      } else if (hasConflict && opts.yes) {
+        // --yes flag: default to override behavior for conflicts
+        writeMode = "override";
+        const repoPath = normalizeRepoPath(selectedRepo.git_repo_resource_path);
+        overrideKey = constructOverrideKey(
+          workspace.remote,
+          workspace.workspaceId,
+          repoPath,
+        );
+        log.info(colors.yellow("Settings conflict detected. Using --override behavior (default for --yes)."));
       } else if (hasConflict) {
         // Non-interactive mode with conflicts - show message and exit
         if (opts.jsonOutput) {
@@ -664,11 +845,19 @@ async function pullGitSyncSettings(
     // Apply the settings based on write mode
     let updatedConfig: SyncOptions;
 
+    // Log which settings mode is being used
+    const repoPath = selectedRepo.git_repo_resource_path.replace(/^\$res:/, "");
+    if (writeMode === "override") {
+      log.info(`Applied repository-specific overrides for repository "${repoPath}"`);
+    } else {
+      log.info(`Applied settings for repository "${repoPath}"`);
+    }
+
     if (writeMode === "replace") {
       // Preserve existing local config and update only git-sync fields
       updatedConfig = { ...localConfig };
-      // Remove overrides since we're in replace mode
-      delete updatedConfig.overrides;
+      // Clear overrides since we're in replace mode, but keep empty object for consistency
+      updatedConfig.overrides = {};
       // Update with backend git-sync settings
       Object.assign(updatedConfig, backendSyncOptions);
     } else if (writeMode === "override" && overrideKey) {
@@ -761,6 +950,7 @@ async function pushGitSyncSettings(
     diff?: boolean;
     jsonOutput?: boolean;
     withBackendSettings?: string;
+    yes?: boolean;
   },
 ) {
   const workspace = await resolveWorkspace(opts);
@@ -888,21 +1078,23 @@ async function pushGitSyncSettings(
     }
 
     // Find the repository to work with
-    let selectedRepo: GitSyncRepository;
-    if (opts.repository) {
-      const found = settings.git_sync.repositories.find(
-        (r: GitSyncRepository) =>
-          r.git_repo_resource_path === opts.repository ||
-          r.git_repo_resource_path === `$res:${opts.repository}`,
-      );
-      if (!found) {
-        throw new Error(`Repository ${opts.repository} not found`);
-      }
-      selectedRepo = found;
-    } else {
-      selectedRepo = await selectRepository(
-        settings.git_sync.repositories,
-      );
+    let selectedRepo = await selectAndLogRepository(
+      settings.git_sync.repositories,
+      opts.repository,
+    );
+
+    // Check if the selected repository needs migration and handle it
+    selectedRepo = await handleLegacyRepositoryMigration(
+      selectedRepo,
+      settings.git_sync,
+      workspace,
+      opts,
+      "push"
+    );
+
+    // If migration was cancelled, exit
+    if (selectedRepo === null) {
+      return;
     }
 
     // Get effective settings for this workspace/repo
@@ -922,24 +1114,25 @@ async function pushGitSyncSettings(
       extra_include_path: effectiveSettings.extraIncludes || [],
     };
 
+    // Calculate diff for all modes
+    const currentBackend = selectedRepo.settings;
+
+    // Convert current backend settings to SyncOptions for user-friendly display
+    const currentSyncOptions: SyncOptions = {
+      includes: currentBackend.include_path || [],
+      excludes: currentBackend.exclude_path || [],
+      extraIncludes: currentBackend.extra_include_path || [],
+      ...includeTypeToSyncOptions(currentBackend.include_type || []),
+    };
+
+    const normalizedCurrent = normalizeSyncOptions(currentSyncOptions);
+    const normalizedEffective = normalizeSyncOptions(effectiveSettings);
+    const gitSyncCurrent = extractGitSyncFields(normalizedCurrent);
+    const gitSyncEffective = extractGitSyncFields(normalizedEffective);
+    const hasChanges = !deepEqual(gitSyncEffective, gitSyncCurrent);
+
     if (opts.diff) {
-      // Show what would be pushed
-      const currentBackend = selectedRepo.settings;
-
-      // Convert current backend settings to SyncOptions for user-friendly display
-      const currentSyncOptions: SyncOptions = {
-        includes: currentBackend.include_path || [],
-        excludes: currentBackend.exclude_path || [],
-        extraIncludes: currentBackend.extra_include_path || [],
-        ...includeTypeToSyncOptions(currentBackend.include_type || []),
-      };
-
-      const normalizedCurrent = normalizeSyncOptions(currentSyncOptions);
-      const normalizedEffective = normalizeSyncOptions(effectiveSettings);
-      const gitSyncCurrent = extractGitSyncFields(normalizedCurrent);
-      const gitSyncEffective = extractGitSyncFields(normalizedEffective);
-      const hasChanges = !deepEqual(gitSyncEffective, gitSyncCurrent);
-
+      // --diff flag: show differences and exit
       if (opts.jsonOutput) {
         // Generate structured diff using the same normalized objects
         const structuredDiff = hasChanges
@@ -958,7 +1151,7 @@ async function pushGitSyncSettings(
         );
       } else {
         if (hasChanges) {
-          log.info("Changes that would be pushed:");
+          log.info("Changes that would be pushed to Windmill:");
           const changes = generateChanges(
             normalizedCurrent,
             normalizedEffective,
@@ -976,6 +1169,39 @@ async function pushGitSyncSettings(
       return;
     }
 
+    // Default behavior: show changes and ask for confirmation (unless --yes is passed)
+    if (hasChanges) {
+      if (!opts.jsonOutput) {
+        const changes = generateChanges(
+          normalizedCurrent,
+          normalizedEffective,
+        );
+
+        if (Object.keys(changes).length === 0) {
+          log.info(colors.green("No changes to push"));
+          return;
+        } else {
+          log.info("Changes that would be pushed to Windmill:");
+          displayChanges(changes);
+        }
+      }
+
+      // Ask for confirmation unless --yes is passed or not in TTY
+      if (!opts.yes && Deno.stdin.isTerminal()) {
+        const confirmed = await Confirm.prompt({
+          message: `Do you want to apply these changes to the remote?`,
+          default: true,
+        });
+
+        if (!confirmed) {
+          return;
+        }
+      }
+    } else {
+      log.info(colors.green("No changes to push"));
+      return;
+    }
+
     if (opts.withBackendSettings) {
       // Skip backend update when using simulated settings
       if (opts.jsonOutput) {
@@ -1104,6 +1330,7 @@ const command = new Command()
     "--with-backend-settings <json:string>",
     "Use provided JSON settings instead of querying backend (for testing)",
   )
+  .option("--yes", "Skip interactive prompts and use default behavior")
   .action(pullGitSyncSettings as any)
   .command("push")
   .description(
@@ -1119,6 +1346,7 @@ const command = new Command()
     "--with-backend-settings <json:string>",
     "Use provided JSON settings instead of querying backend (for testing)",
   )
+  .option("--yes", "Skip interactive prompts and use default behavior")
   .action(pushGitSyncSettings as any);
 
 export { pullGitSyncSettings, pushGitSyncSettings };

cli/main.ts

@@ -143,6 +143,7 @@ const command = new Command()
                     skipFolders: DEFAULT_SYNC_OPTIONS.skipFolders,
                     includeSchedules: DEFAULT_SYNC_OPTIONS.includeSchedules,
                     includeTriggers: DEFAULT_SYNC_OPTIONS.includeTriggers,
+                    overrides: {},
                 };
 
                 await Deno.writeTextFile(

cli/sync.ts

@@ -56,43 +56,8 @@ function mergeCliWithEffectiveOptions<T extends GlobalOptions & SyncOptions & {
   cliOpts: T,
   effectiveOpts: SyncOptions
 ): T {
-  // Start with effective options from config, then overlay only explicitly provided CLI flags
-  const mergedOpts = Object.assign({}, effectiveOpts) as T;
-
-  // Always preserve these operational CLI flags
-  if (cliOpts.dryRun !== undefined) mergedOpts.dryRun = cliOpts.dryRun;
-  if (cliOpts.yes !== undefined) mergedOpts.yes = cliOpts.yes;
-  if (cliOpts.stateful !== undefined) mergedOpts.stateful = cliOpts.stateful;
-  if (cliOpts.skipPull !== undefined) mergedOpts.skipPull = cliOpts.skipPull;
-  if (cliOpts.failConflicts !== undefined) mergedOpts.failConflicts = cliOpts.failConflicts;
-  if (cliOpts.plainSecrets !== undefined) mergedOpts.plainSecrets = cliOpts.plainSecrets;
-  if (cliOpts.json !== undefined) mergedOpts.json = cliOpts.json;
-  if (cliOpts.message !== undefined) mergedOpts.message = cliOpts.message;
-  if (cliOpts.parallel !== undefined) mergedOpts.parallel = cliOpts.parallel;
-  if (cliOpts.jsonOutput !== undefined) mergedOpts.jsonOutput = cliOpts.jsonOutput;
-  if (cliOpts.repository !== undefined) mergedOpts.repository = cliOpts.repository;
-
-  // Always preserve CLI include flags (they should override config file settings)
-  if (cliOpts.includeUsers !== undefined) mergedOpts.includeUsers = cliOpts.includeUsers;
-  if (cliOpts.includeGroups !== undefined) mergedOpts.includeGroups = cliOpts.includeGroups;
-  if (cliOpts.includeSettings !== undefined) mergedOpts.includeSettings = cliOpts.includeSettings;
-  if (cliOpts.includeKey !== undefined) mergedOpts.includeKey = cliOpts.includeKey;
-  if (cliOpts.includeSchedules !== undefined) mergedOpts.includeSchedules = cliOpts.includeSchedules;
-  if (cliOpts.includeTriggers !== undefined) mergedOpts.includeTriggers = cliOpts.includeTriggers;
-
-  // Always preserve CLI skip flags (they should override config file settings)
-  if (cliOpts.skipScripts !== undefined) mergedOpts.skipScripts = cliOpts.skipScripts;
-  if (cliOpts.skipFolders !== undefined) mergedOpts.skipFolders = cliOpts.skipFolders;
-  if (cliOpts.skipVariables !== undefined) mergedOpts.skipVariables = cliOpts.skipVariables;
-  if (cliOpts.skipResources !== undefined) mergedOpts.skipResources = cliOpts.skipResources;
-  if (cliOpts.skipResourceTypes !== undefined) mergedOpts.skipResourceTypes = cliOpts.skipResourceTypes;
-  if (cliOpts.skipSecrets !== undefined) mergedOpts.skipSecrets = cliOpts.skipSecrets;
-  if (cliOpts.skipFlows !== undefined) mergedOpts.skipFlows = cliOpts.skipFlows;
-  if (cliOpts.skipApps !== undefined) mergedOpts.skipApps = cliOpts.skipApps;
-
-
-
-  return mergedOpts;
+  // overlay CLI options on top (undefined cliOpts won't override effectiveOpts)
+  return Object.assign({}, effectiveOpts, cliOpts) as T;
 }
 
 // Resolve effective sync options with smart repository detection
@@ -164,12 +129,14 @@ async function resolveEffectiveSyncOptions(
       } else {
         // Non-interactive mode - list options and use top-level
         log.warn(`Multiple repository overrides found: ${applicableRepos.join(', ')}`);
-        log.warn(`Use --repository flag to specify which one to use. Using top-level settings.`);
+        log.warn(`Running in non-interactive mode. Use --repository flag to specify which one to use.`);
+        log.info(`Falling back to top-level settings (no repository-specific overrides applied)`);
       }
     }
   }
 
   // No repository overrides found or selected - use top-level settings
+  log.info(`No repository overrides found, using top-level settings`);
   return getEffectiveSettings(
     localConfig,
     workspace.remote,

cli/test/gitsync_settings_features.test.ts

@@ -55,7 +55,7 @@ excludes: []`);
     // Read updated config
     const updatedConfig = await Deno.readTextFile(`${tempDir}/wmill.yaml`);
     const backendUrl = new URL(backend.baseUrl).toString();
-    
+
     // Should create workspace wildcard override
     assertStringIncludes(updatedConfig, `'${backendUrl}:${backend.workspace}:*':`);
     assertStringIncludes(updatedConfig, "overrides:");
@@ -109,14 +109,14 @@ skipVariables: false`);
 
     // Read updated config
     const updatedConfig = await Deno.readTextFile(`${tempDir}/wmill.yaml`);
-    
+
     // Should update top-level settings, not create overrides
     assertStringIncludes(updatedConfig, "includes:\n  - f/special/**");
     assertStringIncludes(updatedConfig, "excludes:\n  - '*.test.ts'");
     assertStringIncludes(updatedConfig, "extraIncludes:\n  - g/**");
-    
-    // Should NOT have overrides section
-    assertEquals(updatedConfig.includes("overrides:"), false, "Default mode should not create overrides");
+
+    // Should have empty overrides section for consistency
+    assertStringIncludes(updatedConfig, "overrides: {}", "Should have empty overrides section for consistency");
   });
 });
 
@@ -168,10 +168,10 @@ skipResources: false`);
     ], tempDir);
 
     assertEquals(result.code, 0);
-    
+
     // Should show differences
-    assertStringIncludes(result.stdout, "Changes that would be made:");
+    assertStringIncludes(result.stdout, "Changes that would be applied locally:");
     // Should show the change for skipResources (ignoring ANSI color codes)
     assertStringIncludes(result.stdout, "skipResources:");
   });
-});
+});

cli/test/init_no_git_sync.test.ts

@@ -126,8 +126,8 @@ Deno.test("Init: --use-backend flag applies git-sync settings", async () => {
     assertStringIncludes(wmillYaml, "*.test.ts", "Should include backend's exclude_path");
     assertStringIncludes(wmillYaml, "g/**", "Should include backend's extra_include_path");
     
-    // Should NOT have overrides section since we're starting fresh
-    assertEquals(wmillYaml.includes("overrides:"), false, "Init should not create overrides section");
+    // Should have empty overrides section for consistency
+    assertStringIncludes(wmillYaml, "overrides: {}");
   });
 });
 
@@ -180,6 +180,6 @@ Deno.test("Init: --use-default bypasses backend settings check", async () => {
     
     // Should NOT have backend-specific settings
     assertEquals(wmillYaml.includes("f/should-be-ignored/**"), false, "Should not include backend settings");
-    assertEquals(wmillYaml.includes("overrides:"), false, "Should not create overrides when using defaults");
+    assertStringIncludes(wmillYaml, "overrides: {}", "Should have empty overrides section for consistency");
   });
 });

cli/test/multi_instance_workspace.test.ts

@@ -24,7 +24,7 @@ Deno.test("Multi-Instance: gitsync-settings pull with new format", async () => {
   await withContainerizedBackend(async (backend, tempDir) => {
     // Set up workspace profile
     await setupWorkspaceProfile(backend, "multi_instance_test");
-    
+
     // Create wmill.yaml with new format overrides for different instances
     const backendUrl = new URL(backend.baseUrl).toString(); // Normalize URL
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
@@ -38,22 +38,22 @@ overrides:
     includeTriggers: true
     includeSchedules: true
     skipVariables: true
-  
+
   # Different instance (won't match)
   "https://app.windmill.dev/:${backend.workspace}:u/test/test_repo":
     includeTriggers: false
     includeSchedules: false
     skipVariables: false`);
-    
+
     // Pull settings - should use the matching instance override (skipVariables: true)
     const pullResult = await backend.runCLICommand([
       'gitsync-settings', 'pull',
       '--repository', 'u/test/test_repo',
       '--diff'
     ], tempDir, "multi_instance_test");
-    
+
     assertEquals(pullResult.code, 0);
-    assertStringIncludes(pullResult.stdout, "Changes that would be made:");
+    assertStringIncludes(pullResult.stdout, "Changes that would be applied locally:");
     // includeSchedules should show as a change since backend default is false
     assertStringIncludes(pullResult.stdout, "includeSchedules");
   });
@@ -61,9 +61,9 @@ overrides:
 
 Deno.test("Multi-Instance: gitsync-settings push with overrides", async () => {
   await withContainerizedBackend(async (backend, tempDir) => {
-    // Set up workspace profile  
+    // Set up workspace profile
     await setupWorkspaceProfile(backend, "push_override_test");
-    
+
     // Create wmill.yaml with specific settings that differ from backend defaults
     const backendUrl = new URL(backend.baseUrl).toString();
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
@@ -78,16 +78,16 @@ overrides:
   "${backendUrl}:${backend.workspace}:u/test/test_repo":
     includeSchedules: true
     skipVariables: true`);
-    
+
     // Push settings - should show changes because includeSchedules differs from backend
     const pushResult = await backend.runCLICommand([
       'gitsync-settings', 'push',
       '--repository', 'u/test/test_repo',
       '--diff'
     ], tempDir, "push_override_test");
-    
+
     assertEquals(pushResult.code, 0);
-    assertStringIncludes(pushResult.stdout, "Changes that would be pushed:");
+    assertStringIncludes(pushResult.stdout, "Changes that would be pushed to Windmill:");
     assertStringIncludes(pushResult.stdout, "includeSchedules");
   });
 });
@@ -95,7 +95,7 @@ overrides:
 Deno.test("Multi-Instance: sync with repository-specific overrides", async () => {
   await withContainerizedBackend(async (backend, tempDir) => {
     await setupWorkspaceProfile(backend, "my-workspace_123");
-    
+
     const backendUrl = new URL(backend.baseUrl).toString();
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
@@ -105,22 +105,22 @@ excludes: []
 overrides:
   "${backendUrl}:${backend.workspace}:u/test/test_repo":
     skipApps: true`);
-    
+
     const result = await backend.runCLICommand([
       'sync', 'pull',
       '--repository', 'u/test/test_repo',
       '--dry-run',
       '--json-output'
     ], tempDir, "my-workspace_123");
-    
+
     assertEquals(result.code, 0);
-    
+
     const data = parseJsonFromCLIOutput(result.stdout);
-    
+
     // Test is designed to verify that the new format works correctly
-    
+
     // The test app should NOT appear in changes because skipApps: true
-    const hasTestApp = (data.changes || []).some((change: any) => 
+    const hasTestApp = (data.changes || []).some((change: any) =>
       change.path?.includes('f/test_dashboard')
     );
     assertEquals(hasTestApp, false, "Test app should be skipped due to skipApps override");
@@ -130,7 +130,7 @@ overrides:
 Deno.test("Multi-Instance: auto-detection of single repository override", async () => {
   await withContainerizedBackend(async (backend, tempDir) => {
     await setupWorkspaceProfile(backend, "auto_detect_test");
-    
+
     const backendUrl = new URL(backend.baseUrl).toString();
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
@@ -142,21 +142,21 @@ overrides:
   "${backendUrl}:${backend.workspace}:u/test/test_repo":
     skipApps: true
     includeSchedules: true`);
-    
+
     // Don't specify --repository, it should auto-detect
     const result = await backend.runCLICommand([
       'sync', 'pull',
       '--dry-run',
       '--json-output'
     ], tempDir, "auto_detect_test");
-    
+
     assertEquals(result.code, 0);
     assertStringIncludes(result.stdout, "Auto-selected repository: u/test/test_repo");
-    
+
     const data = parseJsonFromCLIOutput(result.stdout);
-    
+
     // The test app should NOT appear because of auto-detected skipApps: true
-    const hasTestApp = (data.changes || []).some((change: any) => 
+    const hasTestApp = (data.changes || []).some((change: any) =>
       change.path?.includes('f/test_dashboard')
     );
     assertEquals(hasTestApp, false, "Test app should be skipped due to auto-detected override");
@@ -166,7 +166,7 @@ overrides:
 Deno.test("Multi-Instance: workspace wildcards with new format", async () => {
   await withContainerizedBackend(async (backend, tempDir) => {
     await setupWorkspaceProfile(backend, "wildcard_test");
-    
+
     const backendUrl = new URL(backend.baseUrl).toString();
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
@@ -178,22 +178,22 @@ overrides:
   "${backendUrl}:${backend.workspace}:*":
     skipVariables: true
     skipResources: true`);
-    
+
     const result = await backend.runCLICommand([
       'sync', 'pull',
       '--repository', 'u/test/test_repo',
       '--dry-run',
       '--json-output'
     ], tempDir, "wildcard_test");
-    
+
     assertEquals(result.code, 0);
-    
+
     const data = parseJsonFromCLIOutput(result.stdout);
-    
+
     // Variables should be skipped due to wildcard override
-    const hasTestVariable = (data.changes || []).some((change: any) => 
+    const hasTestVariable = (data.changes || []).some((change: any) =>
       change.path?.includes('u/admin/test_config.variable.yaml')
     );
     assertEquals(hasTestVariable, false, "Variables should be skipped due to wildcard override");
   });
-});
+});

cli/test/sync_config_resolution.test.ts

@@ -30,7 +30,7 @@ Deno.test("Integration: wmill.yaml configuration produces expected results", asy
   await withContainerizedBackend(async (backend, tempDir) => {
     // Set up workspace profile with name "localhost_test"
     await setupWorkspaceProfile(backend);
-    
+
     // Create wmill.yaml with settings
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
@@ -43,7 +43,7 @@ skipResources: true
 includeSettings: true
 includeSchedules: true
 includeTriggers: true`);
-    
+
     // Test pull with wmill.yaml configuration
     const yamlResult = await backend.runCLICommand(['sync', 'pull', '--dry-run', '--json-output'], tempDir);
     if (yamlResult.code !== 0) {
@@ -53,21 +53,21 @@ includeTriggers: true`);
       console.log("Stderr:", yamlResult.stderr);
     }
     assertEquals(yamlResult.code, 0);
-    
+
     // Extract JSON from CLI output (skip log messages)
     const yamlData = parseJsonFromCLIOutput(yamlResult.stdout);
-    
+
     // Should include settings.yaml due to includeSettings: true
-    const hasSettings = (yamlData.changes || []).some((change: any) => 
+    const hasSettings = (yamlData.changes || []).some((change: any) =>
       change.type === 'added' && change.path === 'settings.yaml'
     );
     assertEquals(hasSettings, true);
-    
+
     // Should NOT include resources or variables (due to skip flags)
-    const hasResources = (yamlData.changes || []).some((change: any) => 
+    const hasResources = (yamlData.changes || []).some((change: any) =>
       change.type === 'added' && change.path?.includes('.resource.yaml')
     );
-    const hasVariables = (yamlData.changes || []).some((change: any) => 
+    const hasVariables = (yamlData.changes || []).some((change: any) =>
       change.type === 'added' && change.path?.includes('.variable.yaml')
     );
     assertEquals(hasResources, false);
@@ -79,35 +79,35 @@ Deno.test("Integration: settings.yaml inclusion respects includeSettings flag",
   await withContainerizedBackend(async (backend, tempDir) => {
     // Set up workspace profile with name "localhost_test"
     await setupWorkspaceProfile(backend);
-    
-    // Test 1: includeSettings: true should include settings.yaml  
+
+    // Test 1: includeSettings: true should include settings.yaml
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
   - "**"
 includeSettings: true`);
-    
+
     const includeResult = await backend.runCLICommand(['sync', 'pull', '--dry-run', '--json-output'], tempDir);
     assertEquals(includeResult.code, 0);
-    
+
     // Extract JSON from CLI output (skip log messages)
     const includeData = parseJsonFromCLIOutput(includeResult.stdout);
-    const hasSettingsInclude = (includeData.changes || []).some((change: any) => 
+    const hasSettingsInclude = (includeData.changes || []).some((change: any) =>
       change.type === 'added' && change.path === 'settings.yaml'
     );
     assertEquals(hasSettingsInclude, true);
-    
+
     // Test 2: includeSettings: false should NOT include settings.yaml
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
   - "**"
 includeSettings: false`);
-    
+
     const excludeResult = await backend.runCLICommand(['sync', 'pull', '--dry-run', '--json-output'], tempDir);
     assertEquals(excludeResult.code, 0);
-    
+
     // Extract JSON from CLI output (skip log messages)
     const excludeData = parseJsonFromCLIOutput(excludeResult.stdout);
-    const hasSettingsExclude = (excludeData.changes || []).some((change: any) => 
+    const hasSettingsExclude = (excludeData.changes || []).some((change: any) =>
       change.type === 'added' && change.path === 'settings.yaml'
     );
     assertEquals(hasSettingsExclude, false);
@@ -118,30 +118,86 @@ Deno.test("Integration: resource/variable filtering respects skip flags", async
   await withContainerizedBackend(async (backend, tempDir) => {
     // Set up workspace profile with name "localhost_test"
     await setupWorkspaceProfile(backend);
-    
-    // Test skipResources: true  
+
+    // Test skipResources: true
     await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
 includes:
   - "**"
 skipResources: true
 skipVariables: false`);
-    
+
     const result = await backend.runCLICommand(['sync', 'pull', '--dry-run', '--json-output'], tempDir);
     assertEquals(result.code, 0);
-    
+
     // Extract JSON from CLI output (skip log messages)
     const data = parseJsonFromCLIOutput(result.stdout);
-    
+
     // Should NOT include resources
-    const hasResources = (data.changes || []).some((change: any) => 
+    const hasResources = (data.changes || []).some((change: any) =>
       change.type === 'added' && change.path?.includes('.resource.yaml')
     );
     assertEquals(hasResources, false);
-    
+
     // Should include variables (not skipped)
-    const hasVariables = (data.changes || []).some((change: any) => 
+    const hasVariables = (data.changes || []).some((change: any) =>
       change.type === 'added' && change.path?.includes('.variable.yaml')
     );
     assertEquals(hasVariables, true);
   });
-});
+});
+
+// =============================================================================
+// CLI FLAG OVERRIDE TESTS
+// Tests for CLI flags overriding configuration file settings
+// =============================================================================
+
+Deno.test("CLI skip flags override wmill.yaml configuration", async () => {
+  await withContainerizedBackend(async (backend, tempDir) => {
+    // Set up workspace profile with name "localhost_test"
+    await setupWorkspaceProfile(backend);
+
+    // Create wmill.yaml that INCLUDES resources by default (skipResources: false)
+    await Deno.writeTextFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
+includes:
+  - f/**
+  - u/**
+skipResources: false
+skipResourceTypes: false
+includeSettings: true`);
+
+    // Test 1: Without CLI flags - should respect wmill.yaml (include resources)
+    const configResult = await backend.runCLICommand(['sync', 'pull', '--dry-run', '--json-output'], tempDir);
+    assertEquals(configResult.code, 0);
+
+    const configData = parseJsonFromCLIOutput(configResult.stdout);
+
+
+    // Should include resources (not skipped by config)
+    const hasResources = (configData.changes || []).some((change: any) =>
+      change.type === 'added' && change.path?.includes('.resource.yaml')
+    );
+    assertEquals(hasResources, true, "Resources should be included by wmill.yaml config");
+
+    // Test 2: With CLI --skip-resources flag - should override wmill.yaml to skip resources
+    const overrideResult = await backend.runCLICommand([
+      'sync', 'pull', '--dry-run', '--json-output',
+      '--skip-resources',  // CLI flag should override config to skip resources
+      '--skip-resource-types'  // CLI flag should override config to skip resource types
+    ], tempDir);
+    assertEquals(overrideResult.code, 0);
+
+    const overrideData = parseJsonFromCLIOutput(overrideResult.stdout);
+
+    // Should NOT include resources (CLI flag overrides config)
+    const hasResourcesOverride = (overrideData.changes || []).some((change: any) =>
+      change.type === 'added' && change.path?.includes('.resource.yaml')
+    );
+    assertEquals(hasResourcesOverride, false, "CLI --skip-resources flag should override wmill.yaml to exclude resources");
+
+    // Should NOT include resource types (CLI flag overrides config)
+    const hasResourceTypesOverride = (overrideData.changes || []).some((change: any) =>
+      change.type === 'added' && change.path?.includes('.resource-type.yaml')
+    );
+    assertEquals(hasResourceTypesOverride, false, "CLI --skip-resource-types flag should override wmill.yaml to exclude resource types");
+  });
+});

cli/utils.ts

@@ -2,7 +2,7 @@
 // eslint-disable-next-line @typescript-eslint/ban-ts-comment
 // @ts-nocheck This file is copied from a JS project, so it's not type-safe.
 
-import { log, encodeHex, SEP } from "./deps.ts";
+import { colors, log, encodeHex, SEP } from "./deps.ts";
 import crypto from "node:crypto";
 
 export function deepEqual<T>(a: T, b: T): boolean {
@@ -167,7 +167,7 @@ export async function selectRepository<T extends Repository>(
 
   if (repositories.length === 1) {
     const repoPath = repositories[0].git_repo_resource_path.replace(/^\$res:/, "");
-    log.info(`Using repository: ${repoPath}`);
+    log.info(colors.cyan(`Auto-selected repository: ${colors.bold(repoPath)}`));
     return repositories[0];
   }