chore: consolidate Claude Code config to version control

claude-code/CLAUDE.md

@@ -279,3 +279,11 @@ Refer to `claude-config/smartem-decisions/REPO-GUIDELINES.md` for:
 
 - Follow FandanGO plugin conventions
 - Reference peer plugins in repos/FragmentScreen/ for patterns
+
+---
+
+## Git Commit Guidelines
+
+- **No Claude attribution**: Do NOT add `Co-Authored-By: Claude` or any similar attribution lines to commit messages. Commits should appear as normal developer commits.
+- Write clear, concise commit messages following conventional commits format when appropriate (feat, fix, docs, refactor, etc.)
+- Focus on the "why" not the "what" in commit body

core/repos.json

@@ -361,13 +361,13 @@
   ],
   "claudeConfig": {
     "skills": [
-      { "name": "database-admin", "path": "shared/skills/database-admin" },
-      { "name": "devops", "path": "shared/skills/devops" },
-      { "name": "technical-writer", "path": "shared/skills/technical-writer" },
-      { "name": "git", "path": "shared/skills/git" },
-      { "name": "github", "path": "shared/skills/github" },
-      { "name": "ascii-art", "path": "shared/skills/ascii-art" },
-      { "name": "playwright-skill", "path": "smartem-frontend/skills/playwright-skill" }
+      { "name": "database-admin", "path": "claude-code/shared/skills/database-admin" },
+      { "name": "devops", "path": "claude-code/shared/skills/devops" },
+      { "name": "technical-writer", "path": "claude-code/shared/skills/technical-writer" },
+      { "name": "git", "path": "claude-code/shared/skills/git" },
+      { "name": "github", "path": "claude-code/shared/skills/github" },
+      { "name": "ascii-art", "path": "claude-code/shared/skills/ascii-art" },
+      { "name": "playwright-skill", "path": "claude-code/smartem-frontend/skills/playwright-skill" }
     ],
     "defaultPermissions": {
       "allow": [

packages/smartem-workspace/README.md

@@ -44,20 +44,44 @@ smartem-workspace init --preset full --no-interactive
 | `aria-reference` | ARIA ecosystem repos for reference |
 | `minimal` | Just smartem-devtools (workspace setup only) |
 
-### Other commands
+### Verify workspace setup
 
 ```bash
-# Sync existing repos (git pull)
+# Check all configuration
+smartem-workspace check
+
+# Check specific scope
+smartem-workspace check --scope claude
+smartem-workspace check --scope repos
+smartem-workspace check --scope serena
+
+# Auto-repair fixable issues (broken symlinks, missing dirs)
+smartem-workspace check --fix
+```
+
+### Sync repositories
+
+```bash
+# Pull latest from all cloned repos
 smartem-workspace sync
 
-# Show workspace status
+# Preview what would be pulled
+smartem-workspace sync --dry-run
+```
+
+Sync skips repos with uncommitted changes or not on main/master branch.
+
+### Other commands
+
+```bash
+# Show workspace status (alias for check)
 smartem-workspace status
 
-# Add a single repo
+# Add a single repo (not yet implemented)
 smartem-workspace add DiamondLightSource/smartem-frontend
 ```
 
-### Options
+### Init options
 
 ```
 --path PATH         Target directory (default: current directory)
@@ -68,6 +92,20 @@ smartem-workspace add DiamondLightSource/smartem-frontend
 --skip-serena       Skip Serena MCP setup
 ```
 
+### Check options
+
+```
+--scope SCOPE       Check scope: claude, repos, serena, or all (default: all)
+--fix               Attempt to fix issues (recreate symlinks, dirs)
+--offline           Use bundled config instead of fetching from GitHub
+```
+
+### Sync options
+
+```
+--dry-run, -n       Show what would be done without making changes
+```
+
 ## What it sets up
 
 1. **Repository clones** - Organized by organization (DiamondLightSource, FragmentScreen, GitlabAriaPHP)

packages/smartem-workspace/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "smartem-workspace"
-version = "0.1.0"
+version = "0.2.0"
 description = "CLI tool to automate SmartEM multi-repo workspace setup"
 readme = "README.md"
 license = "Apache-2.0"

packages/smartem-workspace/smartem_workspace/cli.py

@@ -6,8 +6,16 @@
 import typer
 from rich.console import Console
 
+from smartem_workspace.commands.check import (
+    CheckScope,
+    apply_fixes,
+    print_report,
+    run_checks,
+)
+from smartem_workspace.commands.sync import print_sync_results, sync_all_repos
 from smartem_workspace.config.loader import load_config
 from smartem_workspace.setup.bootstrap import bootstrap_workspace
+from smartem_workspace.utils.paths import find_workspace_root
 
 app = typer.Typer(
     name="smartem-workspace",
@@ -67,17 +75,138 @@ def init(
 
 
 @app.command()
-def sync() -> None:
-    """Sync existing repos (git pull)."""
-    console.print("[yellow]Not implemented yet[/yellow]")
-    raise typer.Exit(1)
+def check(
+    scope: Annotated[
+        str | None,
+        typer.Option("--scope", "-s", help="Check scope: claude, repos, serena, or all"),
+    ] = None,
+    fix: Annotated[
+        bool,
+        typer.Option("--fix", help="Attempt to fix issues"),
+    ] = False,
+    path: Annotated[
+        Path | None,
+        typer.Option("--path", "-p", help="Workspace path (auto-detected if not specified)"),
+    ] = None,
+    offline: Annotated[
+        bool,
+        typer.Option("--offline", help="Use bundled config instead of fetching from GitHub"),
+    ] = False,
+) -> None:
+    """Verify workspace setup and optionally repair issues."""
+    workspace_path = path or find_workspace_root()
+    if workspace_path is None:
+        console.print("[red]Could not find workspace root. Run from within a workspace or specify --path.[/red]")
+        raise typer.Exit(1)
+
+    config = load_config(offline=offline)
+    if config is None:
+        console.print("[red]Failed to load configuration[/red]")
+        raise typer.Exit(1)
+
+    check_scope = CheckScope.ALL
+    if scope:
+        try:
+            check_scope = CheckScope(scope.lower())
+        except ValueError:
+            console.print(f"[red]Invalid scope: {scope}. Use: claude, repos, serena, or all[/red]")
+            raise typer.Exit(1) from None
+
+    console.print(f"[bold]Checking workspace at {workspace_path}...[/bold]")
+    reports = run_checks(workspace_path, config, check_scope)
+
+    for report in reports:
+        print_report(report)
+
+    total_errors = sum(r.has_errors for r in reports)
+    total_warnings = sum(r.has_warnings for r in reports)
+    total_fixable = sum(r.fixable_count for r in reports)
+
+    console.print()
+    if total_errors or total_warnings:
+        parts = []
+        if total_errors:
+            parts.append(f"[red]{total_errors} error(s)[/red]")
+        if total_warnings:
+            parts.append(f"[yellow]{total_warnings} warning(s)[/yellow]")
+        console.print(f"Summary: {', '.join(parts)}")
+
+        if fix and total_fixable:
+            console.print("\n[bold]Applying fixes...[/bold]")
+            fixed, failed = apply_fixes(workspace_path, reports)
+            console.print(f"\nFixed {fixed} issue(s), {failed} failed")
+            if failed:
+                raise typer.Exit(1)
+        elif total_fixable and not fix:
+            console.print(f"\n[dim]{total_fixable} issue(s) can be fixed with --fix[/dim]")
+            raise typer.Exit(1)
+        else:
+            raise typer.Exit(1)
+    else:
+        console.print("[green]All checks passed![/green]")
 
 
 @app.command()
-def status() -> None:
-    """Show workspace status."""
-    console.print("[yellow]Not implemented yet[/yellow]")
-    raise typer.Exit(1)
+def sync(
+    dry_run: Annotated[
+        bool,
+        typer.Option("--dry-run", "-n", help="Show what would be done without making changes"),
+    ] = False,
+    path: Annotated[
+        Path | None,
+        typer.Option("--path", "-p", help="Workspace path (auto-detected if not specified)"),
+    ] = None,
+) -> None:
+    """Pull latest changes from all cloned repositories."""
+    workspace_path = path or find_workspace_root()
+    if workspace_path is None:
+        console.print("[red]Could not find workspace root. Run from within a workspace or specify --path.[/red]")
+        raise typer.Exit(1)
+
+    config = load_config()
+    if config is None:
+        console.print("[red]Failed to load configuration[/red]")
+        raise typer.Exit(1)
+
+    console.print("[bold blue]SmartEM Workspace Sync[/bold blue]")
+    console.print(f"Workspace: {workspace_path}")
+
+    results = sync_all_repos(workspace_path, config, dry_run=dry_run)
+    print_sync_results(results)
+
+    errors = sum(1 for r in results if r.status == "error")
+    if errors:
+        raise typer.Exit(1)
+
+    if dry_run:
+        would_update = sum(1 for r in results if r.status == "dry-run")
+        if would_update:
+            console.print("\n[dim]Run without --dry-run to apply changes[/dim]")
+
+
+@app.command()
+def status(
+    path: Annotated[
+        Path | None,
+        typer.Option("--path", "-p", help="Workspace path"),
+    ] = None,
+) -> None:
+    """Show workspace status (alias for check --scope all)."""
+    workspace_path = path or find_workspace_root()
+    if workspace_path is None:
+        console.print("[red]Could not find workspace root.[/red]")
+        raise typer.Exit(1)
+
+    config = load_config()
+    if config is None:
+        console.print("[red]Failed to load configuration[/red]")
+        raise typer.Exit(1)
+
+    console.print(f"[bold]Workspace Status: {workspace_path}[/bold]")
+    reports = run_checks(workspace_path, config, CheckScope.ALL)
+
+    for report in reports:
+        print_report(report)
 
 
 @app.command()

packages/smartem-workspace/smartem_workspace/commands/__init__.py

@@ -0,0 +1,13 @@
+"""Command implementations for smartem-workspace CLI."""
+
+from smartem_workspace.commands.check import CheckReport, CheckResult, CheckScope, run_checks
+from smartem_workspace.commands.sync import SyncResult, sync_all_repos
+
+__all__ = [
+    "CheckReport",
+    "CheckResult",
+    "CheckScope",
+    "SyncResult",
+    "run_checks",
+    "sync_all_repos",
+]