🔧 Refactor update command and move audit to upgrade

.github/workflows/ci.yml

@@ -496,10 +496,10 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
         run: |
-          echo "Testing update command to ensure it runs without issues..."
-          # Run update with verbose flag to check for updates without making changes
-          # The command checks for gh-aw updates, action updates, and workflow updates
-          ./gh-aw update --verbose --no-actions
+          echo "Testing update command to ensure it runs successfully..."
+          # Run update with verbose flag to check for and apply workflow updates from source repositories
+          # The command may modify workflow files if upstream updates are available
+          ./gh-aw update --verbose
           echo "✅ Update command executed successfully" >> $GITHUB_STEP_SUMMARY
 
   build:
@@ -1143,7 +1143,7 @@ jobs:
         run: |
           echo "## Dependency Health Audit" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          ./gh-aw update --audit 2>&1 | tee audit_output.txt || true
+          ./gh-aw upgrade --audit 2>&1 | tee audit_output.txt || true
           echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
           head -100 audit_output.txt >> $GITHUB_STEP_SUMMARY
           echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
@@ -1152,7 +1152,7 @@ jobs:
         id: audit_json
         run: |
           # Run audit with JSON output for agent-friendly parsing
-          ./gh-aw update --audit --json > audit.json 2>&1
+          ./gh-aw upgrade --audit --json > audit.json 2>&1
 
           # Display summary in GitHub Actions
           echo "✅ Dependency audit completed" >> $GITHUB_STEP_SUMMARY

docs/src/content/docs/guides/packaging-imports.md

@@ -50,7 +50,7 @@ gh aw update ci-doctor                 # update specific workflow
 gh aw update ci-doctor issue-triage    # update multiple
 ```
 
-Use `--major`, `--force`, `--engine`, or `--verbose` flags to control update behavior. Semantic versions (e.g., `v1.2.3`) update to latest compatible release within same major version. Branch references update to latest commit. Updates use 3-way merge; when conflicts occur, manually resolve conflict markers and run `gh aw compile`.
+Use `--major`, `--force`, `--no-merge`, `--engine`, or `--verbose` flags to control update behavior. Semantic versions (e.g., `v1.2.3`) update to latest compatible release within same major version. Branch references update to latest commit. SHA references update to the latest commit on the default branch. Updates use 3-way merge by default to preserve local changes; use `--no-merge` to replace with the upstream version. When merge conflicts occur, manually resolve conflict markers and run `gh aw compile`.
 
 ## Imports
 

docs/src/content/docs/setup/cli.md

@@ -385,15 +385,16 @@ gh aw remove my-workflow
 
 #### `update`
 
-Update workflows based on `source` field (`owner/repo/path@ref`). Default replaces local file; `--merge` performs 3-way merge. Semantic versions update within same major version.
+Update workflows based on `source` field (`owner/repo/path@ref`). By default, performs a 3-way merge to preserve local changes; use `--no-merge` to override with upstream. Semantic versions update within same major version.
 
 ```bash wrap
 gh aw update                              # Update all with source field
-gh aw update ci-doctor --merge            # Update with 3-way merge
+gh aw update ci-doctor                    # Update specific workflow (3-way merge)
+gh aw update ci-doctor --no-merge         # Override local changes with upstream
 gh aw update ci-doctor --major --force    # Allow major version updates
 ```
 
-**Options:** `--dir`, `--merge`, `--major`, `--force`
+**Options:** `--dir`, `--no-merge`, `--major`, `--force`, `--engine`, `--no-stop-after`, `--stop-after`
 
 #### `upgrade`
 
@@ -404,9 +405,11 @@ gh aw upgrade                              # Upgrade repository agent files and
 gh aw upgrade --no-fix                     # Update agent files only (skip codemods)
 gh aw upgrade --push                       # Upgrade and automatically commit/push
 gh aw upgrade --push --no-fix              # Update agent files and push
+gh aw upgrade --audit                      # Run dependency health audit
+gh aw upgrade --audit --json               # Dependency audit in JSON format
 ```
 
-**Options:** `--dir`, `--no-fix`, `--push` (see [--push flag](#the---push-flag))
+**Options:** `--dir`, `--no-fix`, `--no-actions`, `--push` (see [--push flag](#the---push-flag)), `--audit`, `--json`
 
 ### Advanced
 

pkg/cli/update_command.go

@@ -2,9 +2,7 @@ package cli
 
 import (
 	"fmt"
-	"os"
 
-	"github.com/github/gh-aw/pkg/console"
 	"github.com/github/gh-aw/pkg/constants"
 	"github.com/github/gh-aw/pkg/logger"
 	"github.com/spf13/cobra"
@@ -16,97 +14,59 @@ var updateLog = logger.New("cli:update_command")
 func NewUpdateCommand(validateEngine func(string) error) *cobra.Command {
 	cmd := &cobra.Command{
 		Use:   "update [workflow]...",
-		Short: "Update agentic workflows from their source repositories and check for gh aw updates",
-		Long: `Update one or more workflows from their source repositories and check for gh aw updates.
+		Short: "Update agentic workflows from their source repositories",
+		Long: `Update one or more workflows from their source repositories.
 
-The command:
-1. Checks if a newer version of gh aw is available
-2. Updates GitHub Actions versions in .github/aw/actions-lock.json (unless --no-actions is set)
-3. Updates workflows using the 'source' field in the workflow frontmatter
-4. Compiles each workflow immediately after update
-5. Applies automatic fixes (codemods) to ensure workflows follow latest best practices
+The update command fetches the latest version of each workflow from its source
+repository, merges upstream changes with any local modifications, and recompiles.
 
-By default, the update command replaces local workflow files with the latest version from the source
-repository, overriding any local changes. Use the --merge flag to preserve local changes by performing
-a 3-way merge between the base version, your local changes, and the latest upstream version.
+If no workflow names are specified, all workflows with a 'source' field are updated.
+
+By default, the update performs a 3-way merge to preserve your local changes.
+Use --no-merge to override local changes with the upstream version.
 
 For workflow updates, it fetches the latest version based on the current ref:
 - If the ref is a tag, it updates to the latest release (use --major for major version updates)
 - If the ref is a branch, it fetches the latest commit from that branch
-- Otherwise, it fetches the latest commit from the default branch
-
-For action updates, it checks each action in .github/aw/actions-lock.json for newer releases
-and updates the SHA to pin to the latest version. Use --no-actions to skip action updates.
-
-DEPENDENCY HEALTH AUDIT:
-Use --audit to check dependency health without performing updates. This includes:
-- Outdated Go dependencies with available updates
-- Security advisories from GitHub Security Advisory API
-- Dependency maturity analysis (v0.x vs stable versions)
-- Comprehensive dependency health report
+- If the ref is a commit SHA, it fetches the latest commit from the default branch
 
-The --audit flag implies --dry-run (no updates performed).
+For extension updates, action updates, agent files, and codemods, use 'gh aw upgrade'.
 
 ` + WorkflowIDExplanation + `
 
 Examples:
-  ` + string(constants.CLIExtensionPrefix) + ` update                    # Check gh aw updates, update actions, and update all workflows
-  ` + string(constants.CLIExtensionPrefix) + ` update ci-doctor         # Check gh aw updates, update actions, and update specific workflow
-  ` + string(constants.CLIExtensionPrefix) + ` update --no-actions      # Skip action updates, only update workflows
-  ` + string(constants.CLIExtensionPrefix) + ` update ci-doctor.md      # Check gh aw updates, update actions, and update specific workflow (alternative format)
-  ` + string(constants.CLIExtensionPrefix) + ` update ci-doctor --major # Allow major version updates
-  ` + string(constants.CLIExtensionPrefix) + ` update --merge           # Update with 3-way merge to preserve local changes
-  ` + string(constants.CLIExtensionPrefix) + ` update --pr              # Create PR with changes
-  ` + string(constants.CLIExtensionPrefix) + ` update --force           # Force update even if no changes
-  ` + string(constants.CLIExtensionPrefix) + ` update --dir custom/workflows  # Update workflows in custom directory
-  ` + string(constants.CLIExtensionPrefix) + ` update --audit           # Check dependency health without updating
-  ` + string(constants.CLIExtensionPrefix) + ` update --dry-run         # Show what would be updated without making changes`,
+  ` + string(constants.CLIExtensionPrefix) + ` update                    # Update all workflows from source
+  ` + string(constants.CLIExtensionPrefix) + ` update repo-assist        # Update a specific workflow
+  ` + string(constants.CLIExtensionPrefix) + ` update repo-assist.md     # Same (alternative format)
+  ` + string(constants.CLIExtensionPrefix) + ` update --no-merge         # Override local changes with upstream
+  ` + string(constants.CLIExtensionPrefix) + ` update repo-assist --major # Allow major version updates
+  ` + string(constants.CLIExtensionPrefix) + ` update --force            # Force update even if no changes
+  ` + string(constants.CLIExtensionPrefix) + ` update --dir custom/workflows  # Update workflows in custom directory`,
 		RunE: func(cmd *cobra.Command, args []string) error {
 			majorFlag, _ := cmd.Flags().GetBool("major")
 			forceFlag, _ := cmd.Flags().GetBool("force")
 			engineOverride, _ := cmd.Flags().GetString("engine")
 			verbose, _ := cmd.Flags().GetBool("verbose")
-			prFlag, _ := cmd.Flags().GetBool("pr")
 			workflowDir, _ := cmd.Flags().GetString("dir")
 			noStopAfter, _ := cmd.Flags().GetBool("no-stop-after")
 			stopAfter, _ := cmd.Flags().GetString("stop-after")
-			mergeFlag, _ := cmd.Flags().GetBool("merge")
-			noActions, _ := cmd.Flags().GetBool("no-actions")
-			auditFlag, _ := cmd.Flags().GetBool("audit")
-			dryRunFlag, _ := cmd.Flags().GetBool("dry-run")
-			jsonOutput, _ := cmd.Flags().GetBool("json")
+			noMergeFlag, _ := cmd.Flags().GetBool("no-merge")
 
 			if err := validateEngine(engineOverride); err != nil {
 				return err
 			}
 
-			// Handle audit mode
-			if auditFlag {
-				return runDependencyAudit(verbose, jsonOutput)
-			}
-
-			// Handle dry-run mode
-			if dryRunFlag {
-				// TODO: Implement dry-run mode for workflow updates
-				return fmt.Errorf("--dry-run mode not yet implemented for workflow updates")
-			}
-
-			return UpdateWorkflowsWithExtensionCheck(args, majorFlag, forceFlag, verbose, engineOverride, prFlag, workflowDir, noStopAfter, stopAfter, mergeFlag, noActions)
+			return RunUpdateWorkflows(args, majorFlag, forceFlag, verbose, engineOverride, workflowDir, noStopAfter, stopAfter, noMergeFlag)
 		},
 	}
 
 	cmd.Flags().Bool("major", false, "Allow major version updates when updating tagged releases")
 	cmd.Flags().BoolP("force", "f", false, "Force update even if no changes are detected")
 	addEngineFlag(cmd)
-	cmd.Flags().Bool("pr", false, "Create a pull request with the workflow changes")
 	cmd.Flags().StringP("dir", "d", "", "Workflow directory (default: .github/workflows)")
 	cmd.Flags().Bool("no-stop-after", false, "Remove any stop-after field from the workflow")
 	cmd.Flags().String("stop-after", "", "Override stop-after value in the workflow (e.g., '+48h', '2025-12-31 23:59:59')")
-	cmd.Flags().Bool("merge", false, "Merge local changes with upstream updates instead of overriding")
-	cmd.Flags().Bool("no-actions", false, "Skip updating GitHub Actions versions")
-	cmd.Flags().Bool("audit", false, "Check dependency health without performing updates (implies --dry-run)")
-	cmd.Flags().Bool("dry-run", false, "Show what would be updated without making changes")
-	cmd.Flags().BoolP("json", "j", false, "Output audit results in JSON format (only with --audit)")
+	cmd.Flags().Bool("no-merge", false, "Override local changes with upstream version instead of merging")
 
 	// Register completions for update command
 	cmd.ValidArgsFunction = CompleteWorkflowNames
@@ -116,72 +76,14 @@ Examples:
 	return cmd
 }
 
-// runDependencyAudit performs a dependency health audit
-func runDependencyAudit(verbose bool, jsonOutput bool) error {
-	updateLog.Print("Running dependency health audit")
-
-	// Generate comprehensive report
-	report, err := GenerateDependencyReport(verbose)
-	if err != nil {
-		return fmt.Errorf("failed to generate dependency report: %w", err)
-	}
-
-	// Display the report
-	if jsonOutput {
-		return DisplayDependencyReportJSON(report)
-	}
-	DisplayDependencyReport(report)
+// RunUpdateWorkflows updates workflows from their source repositories.
+// Each workflow is compiled immediately after update.
+func RunUpdateWorkflows(workflowNames []string, allowMajor, force, verbose bool, engineOverride string, workflowsDir string, noStopAfter bool, stopAfter string, noMerge bool) error {
+	updateLog.Printf("Starting update process: workflows=%v, allowMajor=%v, force=%v, noMerge=%v", workflowNames, allowMajor, force, noMerge)
 
-	return nil
-}
-
-// UpdateWorkflowsWithExtensionCheck performs the complete update process:
-// 1. Check for gh-aw extension updates
-// 2. Update GitHub Actions versions (unless --no-actions flag is set)
-// 3. Update workflows from source repositories (compiles each workflow after update)
-// 4. Apply automatic fixes to updated workflows
-// 5. Optionally create a PR
-func UpdateWorkflowsWithExtensionCheck(workflowNames []string, allowMajor, force, verbose bool, engineOverride string, createPR bool, workflowsDir string, noStopAfter bool, stopAfter string, merge bool, noActions bool) error {
-	updateLog.Printf("Starting update process: workflows=%v, allowMajor=%v, force=%v, createPR=%v, merge=%v, noActions=%v", workflowNames, allowMajor, force, createPR, merge, noActions)
-
-	// Step 1: Check for gh-aw extension updates
-	if err := checkExtensionUpdate(verbose); err != nil {
-		return fmt.Errorf("extension update check failed: %w", err)
-	}
-
-	// Step 2: Update GitHub Actions versions (unless disabled)
-	if !noActions {
-		if err := UpdateActions(allowMajor, verbose); err != nil {
-			return fmt.Errorf("action update failed: %w", err)
-		}
-	}
-
-	// Step 3: Update workflows from source repositories
-	// Note: Each workflow is compiled immediately after update
-	if err := UpdateWorkflows(workflowNames, allowMajor, force, verbose, engineOverride, workflowsDir, noStopAfter, stopAfter, merge); err != nil {
+	if err := UpdateWorkflows(workflowNames, allowMajor, force, verbose, engineOverride, workflowsDir, noStopAfter, stopAfter, noMerge); err != nil {
 		return fmt.Errorf("workflow update failed: %w", err)
 	}
 
-	// Step 4: Apply automatic fixes to updated workflows
-	fixConfig := FixConfig{
-		WorkflowIDs: workflowNames,
-		Write:       true,
-		Verbose:     verbose,
-	}
-	if err := RunFix(fixConfig); err != nil {
-		updateLog.Printf("Fix command failed (non-fatal): %v", err)
-		// Don't fail the update if fix fails - this is non-critical
-		if verbose {
-			fmt.Fprintln(os.Stderr, console.FormatWarningMessage(fmt.Sprintf("Warning: automatic fixes failed: %v", err)))
-		}
-	}
-
-	// Step 5: Optionally create PR if flag is set
-	if createPR {
-		if err := createUpdatePR(verbose); err != nil {
-			return fmt.Errorf("failed to create PR: %w", err)
-		}
-	}
-
 	return nil
 }