wafer-cli 0.2.9__py3-none-any.whl → 0.2.11__py3-none-any.whl

wafer/cli.py

@@ -182,7 +182,12 @@ workspaces_app = typer.Typer(
 
 Workspaces are on-demand cloud GPU environments. Requires authentication (wafer login).
 
-  wafer workspaces create dev --gpu H100   # Create workspace
+Available GPUs:
+  MI300X  AMD Instinct MI300X (192GB HBM3, ROCm)
+  B200    NVIDIA Blackwell B200 (180GB HBM3e, CUDA)
+
+Commands:
+  wafer workspaces create dev --gpu B200   # Create workspace
   wafer workspaces exec dev -- python x.py # Run commands
   wafer workspaces ssh dev                 # Interactive SSH
   wafer workspaces sync dev ./project      # Sync files
@@ -190,6 +195,36 @@ Workspaces are on-demand cloud GPU environments. Requires authentication (wafer
 )
 app.add_typer(workspaces_app, name="workspaces")
 
+# SSH Key management (BYOK - Bring Your Own Key)
+ssh_keys_app = typer.Typer(
+    help="""Manage SSH public keys for workspace access.
+
+Register your SSH public keys here. These keys are installed in all workspaces
+you provision, enabling SSH access from any machine with your private key.
+
+  wafer ssh-keys list              # List registered keys
+  wafer ssh-keys add               # Add key (auto-detects ~/.ssh/id_ed25519.pub)
+  wafer ssh-keys add ~/.ssh/id_rsa.pub --name laptop  # Add specific key
+  wafer ssh-keys remove <key-id>   # Remove a key"""
+)
+app.add_typer(ssh_keys_app, name="ssh-keys")
+
+# Target operations (exec/ssh/sync on configured targets)
+targets_ops_app = typer.Typer(
+    help="""Execute commands on configured GPU targets.
+
+Run commands, SSH, or sync files to targets without going through evaluate.
+Useful for exploratory work, debugging, or custom scripts.
+
+  wafer targets exec my-target -- python test.py    # Run command
+  wafer targets ssh my-target                       # Interactive SSH
+  wafer targets sync my-target ./local_dir          # Sync files
+
+Supports: RunPod, DigitalOcean (auto-provisions), SSH targets (baremetal/vm).
+Configure targets with: wafer config targets init ..."""
+)
+app.add_typer(targets_ops_app, name="targets")
+
 # Billing management
 billing_app = typer.Typer(help="Manage billing, credits, and subscription")
 app.add_typer(billing_app, name="billing")
@@ -257,13 +292,100 @@ nvidia_app.add_typer(tracelens_app, name="tracelens")
 amd_app = typer.Typer(help="AMD GPU profiling and analysis tools")
 app.add_typer(amd_app, name="amd")
 
-# ISA analysis - under amd
-isa_app = typer.Typer(help="ISA analysis for AMD GPU code objects (.co files)")
+# Unified ISA Analyzer - supports both .co files and Triton artifacts
+isa_app = typer.Typer(help="ISA analysis for AMD GPU kernels (.co, .s, .ll, .ttgir files)")
 amd_app.add_typer(isa_app, name="isa")
 
-# Kernel Scope - static ISA analysis for Triton kernels
-kernel_scope_app = typer.Typer(help="Static ISA analysis for Triton compilation artifacts")
-amd_app.add_typer(kernel_scope_app, name="kernel-scope")
+# =============================================================================
+# Roofline analysis (wafer roofline)
+# =============================================================================
+
+
+@app.command("roofline")
+def roofline_cmd(
+    gpu: str | None = typer.Option(
+        None, "--gpu", "-g", help="GPU name (e.g., H100, B200, MI300X, A100)"
+    ),
+    bytes_moved: float | None = typer.Option(
+        None, "--bytes", "-b", help="Theoretical minimum bytes moved"
+    ),
+    flops: float | None = typer.Option(None, "--flops", "-f", help="Theoretical minimum FLOPs"),
+    time_ms: float | None = typer.Option(
+        None, "--time-ms", "-t", help="Actual kernel time in milliseconds"
+    ),
+    dtype: str = typer.Option(
+        "fp16", "--dtype", "-d", help="Data type for compute ceiling (fp16, fp32, bf16, fp8, int8)"
+    ),
+    list_gpus: bool = typer.Option(False, "--list-gpus", help="List available GPU specs and exit"),
+) -> None:
+    """Analyze kernel performance against roofline model.
+
+    The roofline model shows the theoretical speed-of-light (SOL) for your kernel
+    based on whether it's memory-bound or compute-bound.
+
+    You need to provide:
+    - The GPU you ran on
+    - Theoretical minimum bytes moved (not actual - what the algorithm requires)
+    - Theoretical minimum FLOPs
+    - Actual measured kernel time
+
+    Example:
+        # Analyze a matmul kernel (4096x4096x4096, FP16)
+        # Theoretical: 2*M*N*K FLOPs = 137.4 TFLOP
+        # Theoretical bytes: (M*K + K*N + M*N) * 2 = 100.7 MB
+        wafer roofline --gpu H100 --bytes 100.7e6 --flops 137.4e12 --time-ms 85
+
+        # Analyze a memory-bound elementwise add (1B elements FP32)
+        # Reads 2 tensors, writes 1 = 12 GB total
+        # 1B adds = 1 GFLOP
+        wafer roofline --gpu H100 --bytes 12e9 --flops 1e9 --time-ms 4 --dtype fp32
+
+        # List available GPUs
+        wafer roofline --list-gpus
+    """
+    from wafer_core.roofline import get_gpu_spec, roofline_analysis
+    from wafer_core.roofline import list_gpus as get_all_gpus
+
+    if list_gpus:
+        typer.echo("Available GPUs:")
+        for name in get_all_gpus():
+            spec = get_gpu_spec(name)
+            typer.echo(
+                f"  {name}: {spec.peak_bandwidth_gbps:.0f} GB/s, {spec.peak_tflops_fp16:.0f} TFLOPS FP16"
+            )
+        return
+
+    # Validate required args for analysis
+    missing = []
+    if gpu is None:
+        missing.append("--gpu")
+    if bytes_moved is None:
+        missing.append("--bytes")
+    if flops is None:
+        missing.append("--flops")
+    if time_ms is None:
+        missing.append("--time-ms")
+
+    if missing:
+        typer.echo(f"Error: Missing required options: {', '.join(missing)}", err=True)
+        typer.echo("", err=True)
+        typer.echo("Run 'wafer roofline --help' for usage.", err=True)
+        raise typer.Exit(1)
+
+    try:
+        result = roofline_analysis(
+            gpu=gpu,
+            dtype=dtype,
+            bytes_moved=bytes_moved,
+            flops=flops,
+            time_ms=time_ms,
+        )
+    except ValueError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    typer.echo(result.format_report())
+
 
 # =============================================================================
 # Skill management (wafer skill ...)
@@ -279,21 +401,22 @@ def skill_install(
         "all",
         "--target",
         "-t",
-        help="Target tool: claude, codex, or all",
+        help="Target tool: claude, codex, cursor, or all",
     ),
     force: bool = typer.Option(False, "--force", "-f", help="Overwrite existing skill"),
 ) -> None:
     """Install the wafer-guide skill for AI coding assistants.
 
     Installs the bundled skill to make wafer commands discoverable by
-    Claude Code and/or OpenAI Codex CLI.
+    Claude Code, OpenAI Codex CLI, and/or Cursor.
 
     Skills follow the open agent skills specification (agentskills.io).
 
     Examples:
-        wafer skill install              # Install for both Claude and Codex
+        wafer skill install              # Install for all tools
         wafer skill install -t claude    # Install for Claude Code only
         wafer skill install -t codex     # Install for Codex CLI only
+        wafer skill install -t cursor    # Install for Cursor only
         wafer skill install --force      # Overwrite existing installation
     """
     # Locate bundled skill
@@ -311,9 +434,13 @@ def skill_install(
         ))
     if target in ("all", "codex"):
         targets_to_install.append(("Codex CLI", Path.home() / ".codex" / "skills" / "wafer-guide"))
+    if target in ("all", "cursor"):
+        targets_to_install.append(("Cursor", Path.home() / ".cursor" / "skills" / "wafer-guide"))
 
     if not targets_to_install:
-        typer.echo(f"Error: Unknown target '{target}'. Use: claude, codex, or all", err=True)
+        typer.echo(
+            f"Error: Unknown target '{target}'. Use: claude, codex, cursor, or all", err=True
+        )
         raise typer.Exit(1)
 
     for tool_name, dest_path in targets_to_install:
@@ -348,14 +475,15 @@ def skill_uninstall(
         "all",
         "--target",
         "-t",
-        help="Target tool: claude, codex, or all",
+        help="Target tool: claude, codex, cursor, or all",
     ),
 ) -> None:
     """Uninstall the wafer-guide skill.
 
     Examples:
-        wafer skill uninstall              # Uninstall from both
+        wafer skill uninstall              # Uninstall from all tools
         wafer skill uninstall -t claude    # Uninstall from Claude Code only
+        wafer skill uninstall -t cursor    # Uninstall from Cursor only
     """
     targets_to_uninstall: list[tuple[str, Path]] = []
 
@@ -369,9 +497,16 @@ def skill_uninstall(
             "Codex CLI",
             Path.home() / ".codex" / "skills" / "wafer-guide",
         ))
+    if target in ("all", "cursor"):
+        targets_to_uninstall.append((
+            "Cursor",
+            Path.home() / ".cursor" / "skills" / "wafer-guide",
+        ))
 
     if not targets_to_uninstall:
-        typer.echo(f"Error: Unknown target '{target}'. Use: claude, codex, or all", err=True)
+        typer.echo(
+            f"Error: Unknown target '{target}'. Use: claude, codex, cursor, or all", err=True
+        )
         raise typer.Exit(1)
 
     for tool_name, dest_path in targets_to_uninstall:
@@ -406,6 +541,7 @@ def skill_status() -> None:
     installations = [
         ("Claude Code", Path.home() / ".claude" / "skills" / "wafer-guide"),
         ("Codex CLI", Path.home() / ".codex" / "skills" / "wafer-guide"),
+        ("Cursor", Path.home() / ".cursor" / "skills" / "wafer-guide"),
     ]
 
     for tool_name, path in installations:
@@ -1114,6 +1250,11 @@ def agent(  # noqa: PLR0913
         "--list-sessions",
         help="List recent sessions and exit",
     ),
+    get_session: str | None = typer.Option(
+        None,
+        "--get-session",
+        help="Get session by ID and print messages (use with --json)",
+    ),
     tools: str | None = typer.Option(
         None,
         "--tools",
@@ -1160,47 +1301,7 @@ def agent(  # noqa: PLR0913
         None,
         "--corpus",
         "-c",
-        help="Documentation corpus to use (cuda, cutlass, hip). Must be downloaded first.",
-    ),
-    # Legacy kernel optimization options (hidden, for backwards compat)
-    problem: Path | None = typer.Option(
-        None,
-        "--problem",
-        hidden=True,
-        help="[Legacy] Path to problem YAML config file",
-    ),
-    reference: Path | None = typer.Option(
-        None,
-        "--reference",
-        "--ref",
-        hidden=True,
-        help="[Legacy] Path to reference kernel file",
-    ),
-    description: str | None = typer.Option(
-        None,
-        "--description",
-        "--desc",
-        hidden=True,
-        help="[Legacy] Problem description",
-    ),
-    test: list[str] | None = typer.Option(
-        None,
-        "--test",
-        hidden=True,
-        help="[Legacy] Test case",
-    ),
-    benchmark: list[str] | None = typer.Option(
-        None,
-        "--benchmark",
-        "-b",
-        hidden=True,
-        help="[Legacy] Benchmark case",
-    ),
-    speedup_target: float | None = typer.Option(
-        None,
-        "--speedup",
-        hidden=True,
-        help="[Legacy] Speedup target",
+        help="Documentation corpus to use (cuda, cutlass, hip, amd). Must be downloaded first.",
     ),
 ) -> None:
     """AI assistant for GPU kernel development.
@@ -1287,20 +1388,15 @@ def agent(  # noqa: PLR0913
         prompt=actual_prompt,
         interactive=use_tui,
         single_turn=single_turn,
-        problem=str(problem) if problem else None,
-        reference=str(reference) if reference else None,
-        description=description,
-        tests=list(test) if test else None,
-        benchmarks=list(benchmark) if benchmark else None,
         model=model,
-        max_turns=max_turns,
-        speedup_target=speedup_target,
         resume=resume,
         from_turn=from_turn,
         list_sessions=list_sessions,
+        get_session=get_session,
         tools=tools.split(",") if tools else None,
         allow_spawn=allow_spawn,
         max_tool_fails=max_tool_fails,
+        max_turns=max_turns,
         json_output=json_output,
         template=template,
         template_args=parsed_template_args,
@@ -1310,7 +1406,7 @@ def agent(  # noqa: PLR0913
 
 # =============================================================================
 # Evaluate command
-# Hidden aliases for backwards compatibility
+# Hidden aliases for agent command
 def _make_agent_alias(name: str, doc: str) -> None:
     """Create a hidden alias that delegates to agent()."""
 
@@ -1325,6 +1421,7 @@ def _make_agent_alias(name: str, doc: str) -> None:
         resume: str | None = typer.Option(None, "--resume", "-r"),
         from_turn: int | None = typer.Option(None, "--from-turn"),
         list_sessions: bool = typer.Option(False, "--list-sessions"),
+        get_session: str | None = typer.Option(None, "--get-session"),
         tools: str | None = typer.Option(None, "--tools"),
         allow_spawn: bool = typer.Option(False, "--allow-spawn"),
         max_tool_fails: int | None = typer.Option(None, "--max-tool-fails"),
@@ -1334,12 +1431,6 @@ def _make_agent_alias(name: str, doc: str) -> None:
         template: str | None = typer.Option(None, "--template", "-t"),
         template_args: list[str] | None = typer.Option(None, "--args"),
         corpus: str | None = typer.Option(None, "--corpus"),
-        problem: Path | None = typer.Option(None, "--problem", hidden=True),
-        reference: Path | None = typer.Option(None, "--reference", hidden=True),
-        description: str | None = typer.Option(None, "--description", hidden=True),
-        test: list[Path] | None = typer.Option(None, "--test", hidden=True),
-        benchmark: list[Path] | None = typer.Option(None, "--benchmark", hidden=True),
-        speedup_target: float | None = typer.Option(None, "--speedup-target", hidden=True),
     ) -> None:
         agent(
             prompt=prompt,
@@ -1349,6 +1440,7 @@ def _make_agent_alias(name: str, doc: str) -> None:
             resume=resume,
             from_turn=from_turn,
             list_sessions=list_sessions,
+            get_session=get_session,
             tools=tools,
             allow_spawn=allow_spawn,
             max_tool_fails=max_tool_fails,
@@ -1358,12 +1450,6 @@ def _make_agent_alias(name: str, doc: str) -> None:
             template=template,
             template_args=template_args,
             corpus=corpus,
-            problem=problem,
-            reference=reference,
-            description=description,
-            test=test,
-            benchmark=benchmark,
-            speedup_target=speedup_target,
         )
 
     alias_cmd.__doc__ = doc
@@ -1649,7 +1735,7 @@ def kernelbench_list_problems() -> None:
 
 
 @kernelbench_app.callback(invoke_without_command=True)
-def kernelbench_evaluate(  # noqa: PLR0913
+def kernelbench_evaluate(  # noqa: PLR0913, PLR0915
     ctx: typer.Context,
     implementation: Path | None = typer.Option(
         None,
@@ -1685,10 +1771,22 @@ def kernelbench_evaluate(  # noqa: PLR0913
     defensive: bool = typer.Option(
         False, "--defensive", help="Enable defensive timing to detect evaluation hacking"
     ),
+    backend: str | None = typer.Option(
+        None,
+        "--backend",
+        help="Kernel backend for static validation (hip, cuda, triton, cute, tilelang, thunderkittens). "
+        "When specified, validates that the implementation uses the correct backend primitives.",
+    ),
     sync_artifacts: bool = typer.Option(
         True, "--sync-artifacts/--no-sync-artifacts", help="Download artifacts"
     ),
     gpu_id: int | None = typer.Option(None, "--gpu-id", help="Override GPU ID"),
+    json_output: bool = typer.Option(
+        False, "--json", help="Output as single JSON object (machine-readable)"
+    ),
+    jsonl_output: bool = typer.Option(
+        False, "--jsonl", help="Output as streaming JSON Lines (one object per event)"
+    ),
 ) -> None:
     """Run kernel evaluation in KernelBench format (ModelNew class).
 
@@ -1744,6 +1842,10 @@ def kernelbench_evaluate(  # noqa: PLR0913
         raise typer.Exit(1)
 
     from .evaluate import KernelBenchEvaluateArgs, run_evaluate_kernelbench
+    from .output import OutputCollector, format_evaluate_result, get_output_format
+
+    output_format = get_output_format(json_output, jsonl_output)
+    collector = OutputCollector(format=output_format)
 
     # If pool specified, acquire a target from the pool
     resolved_target = target or ""
@@ -1756,32 +1858,36 @@ def kernelbench_evaluate(  # noqa: PLR0913
         try:
             pool_targets = get_pool(pool)
         except FileNotFoundError as e:
-            typer.echo(f"Error: {e}", err=True)
+            collector.set_error("pool", "PoolNotFound", pool=pool, message=str(e))
+            collector.finalize()
             raise typer.Exit(1) from None
 
         # Filter to only targets with valid auth
         usable_targets, skipped = filter_pool_by_auth(pool_targets)
         if skipped:
-            typer.echo(f"Skipping targets without auth: {', '.join(skipped)}", err=True)
+            collector.emit("pool_auth_skip", targets=skipped)
 
         if not usable_targets:
-            typer.echo(f"Error: No usable targets in pool '{pool}'", err=True)
-            typer.echo("  All targets require authentication that is not configured.", err=True)
-            typer.echo("  Run 'wafer auth status' to see which providers need setup.", err=True)
+            collector.set_error("pool", "NoUsableTargets", pool=pool)
+            collector.finalize()
             raise typer.Exit(1) from None
 
-        typer.echo(f"Acquiring target from pool '{pool}' ({len(usable_targets)} targets)...")
+        collector.emit("pool_acquire", pool=pool, count=len(usable_targets))
         pool_lock_context = acquire_from_pool(usable_targets)
         acquired_target = pool_lock_context.__enter__()
 
         if acquired_target is None:
-            typer.echo(f"Error: All targets in pool '{pool}' are busy", err=True)
-            typer.echo(f"  Targets: {', '.join(usable_targets)}", err=True)
+            # Exit context manager before raising to avoid resource leak
+            pool_lock_context.__exit__(None, None, None)
+            collector.set_error("pool", "AllTargetsBusy", pool=pool, targets=usable_targets)
+            collector.finalize()
             raise typer.Exit(1)
 
-        typer.echo(f"Acquired target: {acquired_target}")
+        collector.emit("pool_acquired", target=acquired_target)
         resolved_target = acquired_target
 
+    collector.target = resolved_target
+
     args = KernelBenchEvaluateArgs(
         implementation=implementation,
         reference=reference,
@@ -1791,41 +1897,45 @@ def kernelbench_evaluate(  # noqa: PLR0913
         inputs=inputs,
         seed=seed,
         defensive=defensive,
+        backend=backend,
         sync_artifacts=sync_artifacts,
         gpu_id=gpu_id,
     )
 
+    collector.emit("started", target=resolved_target)
+
     try:
         import trio_asyncio
 
+        collector.emit("evaluation", status="running")
         result = trio_asyncio.run(run_evaluate_kernelbench, args)
     except KeyboardInterrupt:
-        typer.echo("\nInterrupted by user", err=True)
+        collector.set_error("evaluation", "Interrupted", message="Interrupted by user")
+        collector.finalize()
         raise typer.Exit(130) from None
     except Exception as e:
-        typer.echo(f"Error: {e}", err=True)
+        collector.set_error("evaluation", "Exception", message=str(e))
+        collector.finalize()
         raise typer.Exit(1) from None
     finally:
         # Release pool lock if we acquired one
         if pool_lock_context is not None:
             pool_lock_context.__exit__(None, None, None)
 
-    # Print results
+    # Build structured output
+    eval_output = format_evaluate_result(result, target=resolved_target)
+    collector._result = eval_output
+
+    # Print results based on output format
     if result.success:
-        typer.echo("")
-        typer.echo("=" * 60)
-        status = "PASS" if result.all_correct else "FAIL"
-        typer.echo(f"Result: {status}")
-        score_pct = f"{result.correctness_score:.1%}"
-        typer.echo(f"Correctness: {result.passed_tests}/{result.total_tests} ({score_pct})")
-        if result.geomean_speedup > 0:
-            typer.echo(f"Speedup: {result.geomean_speedup:.2f}x")
-        typer.echo("=" * 60)
+        collector.output_text_result(result)
+        collector.finalize()
 
         if not result.all_correct:
             raise typer.Exit(1)
     else:
-        typer.echo(f"Error: {result.error_message}", err=True)
+        collector.output_text_error(result.error_message or "Unknown error")
+        collector.finalize()
         raise typer.Exit(1)
 
 
@@ -2182,6 +2292,8 @@ def gpumode_evaluate(  # noqa: PLR0913, PLR0915
         acquired_target = pool_lock_context.__enter__()
 
         if acquired_target is None:
+            # Exit context manager before raising to avoid resource leak
+            pool_lock_context.__exit__(None, None, None)
             typer.echo(f"Error: All targets in pool '{pool}' are busy", err=True)
             typer.echo(f"  Targets: {', '.join(usable_targets)}", err=True)
             raise typer.Exit(1)
@@ -2402,6 +2514,7 @@ def _run_api_mode(  # noqa: PLR0913
     upload_dir: Path | None,
     workspace_id: str | None,
     gpu_id: int | None,
+    gpu_count: int,
     docker_image: str | None,
     docker_entrypoint: str | None,
     pull_image: bool,
@@ -2416,6 +2529,8 @@ def _run_api_mode(  # noqa: PLR0913
         typer.echo(f"Workspace: {workspace_id}")
     if gpu_id is not None:
         typer.echo(f"GPU: {gpu_id}")
+    if gpu_count > 1:
+        typer.echo(f"GPU count: {gpu_count}")
     if docker_image:
         typer.echo(f"Image: {docker_image}")
     if docker_entrypoint:
@@ -2433,6 +2548,7 @@ def _run_api_mode(  # noqa: PLR0913
             upload_dir=upload_dir,
             workspace_id=workspace_id,
             gpu_id=gpu_id,
+            gpu_count=gpu_count,
             docker_image=docker_image,
             docker_entrypoint=docker_entrypoint,
             pull_image=pull_image,
@@ -2456,6 +2572,7 @@ def remote_run(  # noqa: PLR0913
         None, "--workspace-id", "-w", help="Workspace ID (from wafer push)"
     ),
     gpu_id: int | None = typer.Option(None, "--gpu", "-g", help="GPU ID"),
+    gpu_count: int = typer.Option(1, "--gpu-count", "-n", help="Number of GPUs (1-8)"),
     docker_image: str | None = typer.Option(None, "--image", "-i", help="Docker image override"),
     docker_entrypoint: str | None = typer.Option(
         None, "--docker-entrypoint", help="Override Docker entrypoint (e.g., 'bash')"
@@ -2525,6 +2642,7 @@ def remote_run(  # noqa: PLR0913
             upload_dir,
             workspace_id,
             gpu_id,
+            gpu_count,
             docker_image,
             docker_entrypoint,
             pull_image,
@@ -4108,6 +4226,81 @@ def billing_portal(
         raise typer.Exit(1) from None
 
 
+# =============================================================================
+# SSH Keys commands (BYOK - Bring Your Own Key)
+# =============================================================================
+
+
+@ssh_keys_app.command("list")
+def ssh_keys_list(
+    json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
+) -> None:
+    """List all registered SSH public keys.
+
+    Example:
+        wafer ssh-keys list
+        wafer ssh-keys list --json
+    """
+    from .ssh_keys import list_ssh_keys
+
+    try:
+        result = list_ssh_keys(json_output=json_output)
+        typer.echo(result)
+    except RuntimeError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from e
+
+
+@ssh_keys_app.command("add")
+def ssh_keys_add(
+    pubkey_path: Path | None = typer.Argument(
+        None, help="Path to public key file (auto-detects ~/.ssh/id_ed25519.pub if not specified)"
+    ),
+    name: str | None = typer.Option(None, "--name", "-n", help="Friendly name for the key"),
+    json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
+) -> None:
+    """Add an SSH public key.
+
+    If no path is specified, auto-detects keys from ~/.ssh/ in preference order:
+    id_ed25519.pub, id_rsa.pub, id_ecdsa.pub.
+
+    Example:
+        wafer ssh-keys add                              # Auto-detect
+        wafer ssh-keys add ~/.ssh/id_rsa.pub            # Specific file
+        wafer ssh-keys add ~/.ssh/id_ed25519.pub --name laptop
+    """
+    from .ssh_keys import add_ssh_key
+
+    try:
+        result = add_ssh_key(pubkey_path=pubkey_path, name=name, json_output=json_output)
+        typer.echo(result)
+    except RuntimeError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from e
+
+
+@ssh_keys_app.command("remove")
+def ssh_keys_remove(
+    key_id: str = typer.Argument(..., help="UUID of the SSH key to remove"),
+    json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
+) -> None:
+    """Remove an SSH public key.
+
+    Get the key ID from 'wafer ssh-keys list'.
+
+    Example:
+        wafer ssh-keys remove abc123-def456-...
+    """
+    from .ssh_keys import remove_ssh_key
+
+    try:
+        result = remove_ssh_key(key_id=key_id, json_output=json_output)
+        typer.echo(result)
+    except RuntimeError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from e
+
+
 # =============================================================================
 # Workspaces commands
 # =============================================================================
@@ -4136,21 +4329,34 @@ def workspaces_list(
 @workspaces_app.command("create")
 def workspaces_create(
     name: str = typer.Argument(..., help="Workspace name"),
-    gpu_type: str = typer.Option("B200", "--gpu", "-g", help="GPU type (default: B200)"),
+    gpu_type: str = typer.Option("B200", "--gpu", "-g", help="GPU type: MI300X (AMD) or B200 (NVIDIA, default)"),
     image: str | None = typer.Option(None, "--image", "-i", help="Docker image (optional)"),
+    wait: bool = typer.Option(False, "--wait", "-w", help="Wait for provisioning and show SSH credentials"),
     json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
 ) -> None:
     """Create a new workspace.
 
+    Available GPUs:
+        MI300X  AMD Instinct MI300X (192GB HBM3, ROCm)
+        B200    NVIDIA Blackwell B200 (180GB HBM3e, CUDA)
+
     Example:
-        wafer workspaces create my-kernel
-        wafer workspaces create my-kernel --gpu H100
+        wafer workspaces create my-kernel                # B200 (default)
+        wafer workspaces create my-kernel --gpu MI300X   # AMD MI300X
+        wafer workspaces create my-kernel --gpu B200     # NVIDIA B200
         wafer workspaces create my-kernel --image pytorch/pytorch:2.5.1-cuda12.4-cudnn9-devel
+        wafer workspaces create my-kernel --wait
     """
     from .workspaces import create_workspace
 
     try:
-        result = create_workspace(name, gpu_type=gpu_type, image=image, json_output=json_output)
+        result = create_workspace(
+            name,
+            gpu_type=gpu_type,
+            image=image,
+            wait=wait,
+            json_output=json_output,
+        )
         typer.echo(result)
     except RuntimeError as e:
         typer.echo(f"Error: {e}", err=True)
@@ -4160,16 +4366,23 @@ def workspaces_create(
 @workspaces_app.command("delete")
 def workspaces_delete(
     workspace_id: str = typer.Argument(..., help="Workspace ID to delete"),
+    yes: bool = typer.Option(False, "--yes", "-y", help="Skip confirmation prompt"),
     json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
 ) -> None:
     """Delete a workspace.
 
     Example:
         wafer workspaces delete ws_abc123
+        wafer workspaces delete ws_abc123 -y
     """
     from .workspaces import delete_workspace
 
     try:
+        if not yes:
+            confirm = typer.confirm(f"Delete workspace '{workspace_id}'?")
+            if not confirm:
+                typer.echo("Cancelled.")
+                raise typer.Exit(0)
         result = delete_workspace(workspace_id, json_output=json_output)
         typer.echo(result)
     except RuntimeError as e:
@@ -4177,32 +4390,6 @@ def workspaces_delete(
         raise typer.Exit(1) from None
 
 
-@workspaces_app.command("attach")
-def workspaces_attach(
-    workspace_id: str = typer.Argument(..., help="Workspace ID to attach to"),
-    json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
-) -> None:
-    """Attach to a workspace (get SSH credentials).
-
-    This will:
-    1. Start the workspace if needed
-    2. Return SSH connection details
-    3. Save the private key to ~/.wafer/keys/
-
-    Example:
-        wafer workspaces attach ws_abc123
-        wafer workspaces attach ws_abc123 --json
-    """
-    from .workspaces import attach_workspace
-
-    try:
-        result = attach_workspace(workspace_id, json_output=json_output)
-        typer.echo(result)
-    except RuntimeError as e:
-        typer.echo(f"Error: {e}", err=True)
-        raise typer.Exit(1) from None
-
-
 @workspaces_app.command("show")
 def workspaces_show(
     workspace_id: str = typer.Argument(..., help="Workspace ID to show"),
@@ -4224,12 +4411,19 @@ def workspaces_show(
         raise typer.Exit(1) from None
 
 
-@workspaces_app.command("exec", context_settings={"allow_interspersed_args": False})
+@workspaces_app.command(
+    "exec",
+    context_settings={
+        "allow_interspersed_args": False,
+        "ignore_unknown_options": True,
+        "allow_extra_args": True,
+    },
+)
 def workspaces_exec(
+    ctx: typer.Context,
     workspace: str | None = typer.Argument(
         None, help="Workspace name or ID (optional if default set)"
     ),
-    command: list[str] = typer.Argument(..., help="Command to execute"),
     timeout: int | None = typer.Option(
         None,
         "--timeout",
@@ -4247,6 +4441,7 @@ def workspaces_exec(
     baremetal: bool = typer.Option(
         False, "--baremetal", help="Force baremetal target (for hardware counters like ncu/nsys)"
     ),
+    pull_image: bool = typer.Option(False, "--pull-image", help="Pull image on target if missing"),
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show [wafer] status messages"),
     quiet: bool = typer.Option(False, "--quiet", "-q", help="Suppress [wafer] status messages"),
 ) -> None:
@@ -4263,6 +4458,8 @@ def workspaces_exec(
     If workspace is not specified, uses the default workspace from config,
     or the only workspace if you have exactly one.
 
+    IMPORTANT: Options must come before the workspace name.
+
     Examples:
         wafer workspaces exec dev -- python train.py
         wafer workspaces exec dev -- python -c "import torch; print(torch.cuda.is_available())"
@@ -4273,6 +4470,34 @@ def workspaces_exec(
     from .global_config import get_defaults, get_preferences
     from .workspaces import exec_command, resolve_workspace, sync_files
 
+    # Enforce option ordering to avoid treating CLI flags as remote commands
+    known_options = {
+        "--timeout",
+        "-t",
+        "--sync",
+        "-s",
+        "--gpu",
+        "--cpu",
+        "--baremetal",
+        "--pull-image",
+        "--verbose",
+        "-v",
+        "--quiet",
+        "-q",
+        "--help",
+        "-h",
+    }
+    for arg in ctx.args:
+        if arg == "--":
+            break
+        if arg in known_options:
+            typer.echo(
+                "Error: options must come before the workspace name. "
+                "Example: wafer workspaces exec --pull-image dev -- python -V",
+                err=True,
+            )
+            raise typer.Exit(1)
+
     # Validate mutually exclusive routing flags
     routing_flags = sum([gpu, cpu, baremetal])
     if routing_flags > 1:
@@ -4339,27 +4564,30 @@ def workspaces_exec(
             typer.echo(f"Error: {e}", err=True)
             raise typer.Exit(1) from None
 
+    # Get command from context args (passthrough after --)
+    import shlex
+
+    command = list(ctx.args)
+    if command and command[0] == "--":
+        command = command[1:]
+
+    if not command:
+        typer.echo("Error: No command specified", err=True)
+        raise typer.Exit(1)
+
     if show_status:
         typer.echo(f"[wafer] Executing (timeout: {effective_timeout}s)...", err=True)
 
-    # Join command list into shell command string, stripping leading "--" separator
-    if isinstance(command, list):
-        import shlex
-
-        # Remove leading "--" if present (typer passes it through with allow_interspersed_args=False)
-        if command and command[0] == "--":
-            command = command[1:]
-        # Handle two cases:
-        # 1. Single element: user quoted the whole command (e.g., "echo hello world")
-        #    -> use directly, don't re-quote
-        # 2. Multiple elements: user passed separate args (e.g., -- python -c "print(1)")
-        #    -> use shlex.join to properly quote args with spaces
-        if len(command) == 1:
-            command_str = command[0]
-        else:
-            command_str = shlex.join(command)
+    # Build command string
+    # Handle two cases:
+    # 1. Single element: user quoted the whole command (e.g., "echo hello world")
+    #    -> use directly, don't re-quote
+    # 2. Multiple elements: user passed separate args (e.g., -- python -c "print(1)")
+    #    -> use shlex.join to properly quote args with spaces
+    if len(command) == 1:
+        command_str = command[0]
     else:
-        command_str = command
+        command_str = shlex.join(command)
 
     try:
         exit_code = exec_command(
@@ -4367,6 +4595,7 @@ def workspaces_exec(
             command=command_str,
             timeout_seconds=effective_timeout,
             routing=routing,
+            pull_image=pull_image,
         )
     except RuntimeError as e:
         typer.echo(f"Error: {e}", err=True)
@@ -4386,7 +4615,7 @@ def workspaces_ssh(
 ) -> None:
     """SSH into a workspace.
 
-    Gets SSH credentials via attach, then execs into SSH.
+    Uses workspace SSH credentials once the workspace is running.
     If workspace is not specified, uses the default workspace.
 
     Examples:
@@ -4395,7 +4624,7 @@ def workspaces_ssh(
     """
     import os
 
-    from .workspaces import get_ssh_credentials, resolve_workspace
+    from .workspaces import get_workspace_raw, resolve_workspace
 
     # Resolve workspace
     try:
@@ -4406,26 +4635,39 @@ def workspaces_ssh(
 
     typer.echo(f"Connecting to workspace: {resolved_workspace}...", err=True)
 
-    # Get SSH credentials (this calls attach)
+    # Get SSH credentials from workspace
     try:
-        creds = get_ssh_credentials(resolved_workspace)
+        ws = get_workspace_raw(resolved_workspace)
     except RuntimeError as e:
         typer.echo(f"Error: {e}", err=True)
         raise typer.Exit(1) from None
 
-    # Exec into SSH - replaces this process
-    ssh_args = [
-        "ssh",
-        "-i",
-        str(creds.key_path),
+    from .workspaces import VALID_STATUSES
+    
+    workspace_status = ws.get("status")
+    assert workspace_status in VALID_STATUSES, (
+        f"Workspace {resolved_workspace} has invalid status '{workspace_status}'. "
+        f"Valid statuses: {VALID_STATUSES}"
+    )
+    
+    if workspace_status != "running":
+        typer.echo(f"Error: Workspace is {workspace_status}. Wait for it to be running.", err=True)
+        raise typer.Exit(1)
+    if not ws.get("ssh_host") or not ws.get("ssh_port") or not ws.get("ssh_user"):
+        typer.echo("Error: SSH credentials not available yet.", err=True)
+        raise typer.Exit(1)
+
+    # Build SSH args - key_path is None for BYOK model (uses default SSH key)
+    ssh_args = ["ssh"]
+    ssh_args.extend([
         "-p",
-        str(creds.port),
+        str(ws.get("ssh_port")),
         "-o",
         "StrictHostKeyChecking=no",
         "-o",
         "UserKnownHostsFile=/dev/null",
-        f"{creds.user}@{creds.host}",
-    ]
+        f"{ws.get('ssh_user')}@{ws.get('ssh_host')}",
+    ])
 
     # Replace current process with SSH
     os.execvp("ssh", ssh_args)
@@ -4492,51 +4734,568 @@ def workspaces_sync(
 
 
 # =============================================================================
-# Perfetto trace analysis commands
+# Target operations commands (exec/ssh/sync)
 # =============================================================================
 
 
-@perfetto_app.command("query")
-def perfetto_query(
-    trace_path: Path = typer.Argument(..., help="Path to Perfetto trace file"),
-    sql: str = typer.Argument(..., help="SQL query to execute"),
-    json_output: bool = typer.Option(True, "--json", "-j", help="Output as JSON"),
+@targets_ops_app.command("exec", context_settings={"allow_interspersed_args": False})
+def targets_exec(
+    target: str = typer.Argument(
+        ...,
+        help="Target name",
+        autocompletion=complete_target_name,
+    ),
+    command: list[str] = typer.Argument(..., help="Command to execute"),
+    timeout: int | None = typer.Option(
+        None,
+        "--timeout",
+        "-t",
+        help="Execution timeout in seconds (default: 300)",
+    ),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show [wafer] status messages"),
+    quiet: bool = typer.Option(False, "--quiet", "-q", help="Suppress [wafer] status messages"),
 ) -> None:
-    """Execute SQL query against a Perfetto trace.
+    """Execute a command on a configured target.
 
-    Starts trace_processor, loads the trace, executes the query, and returns results.
+    Provisions the target if needed (RunPod, DigitalOcean), then runs the command via SSH.
+    For cloud targets, the instance is kept alive after execution - use
+    'wafer config targets cleanup <name>' to terminate.
+
+    Supported targets: RunPod, DigitalOcean, SSH (baremetal/vm).
+    Not supported: Modal (serverless), Local (no SSH), Workspace (use 'wafer workspaces exec').
 
     Examples:
-        wafer perfetto query trace.perfetto "SELECT * FROM slice LIMIT 10"
-        wafer perfetto query trace.perfetto "SELECT name, dur FROM slice ORDER BY dur DESC LIMIT 5"
+        wafer targets exec runpod-mi300x -- python -c "import torch; print(torch.cuda.is_available())"
+        wafer targets exec runpod-mi300x -- rocm-smi
+        wafer targets exec my-ssh-server -- nvidia-smi
+        wafer targets exec runpod-mi300x "echo hello && ls -la" --timeout 60
     """
-    from wafer_core.lib.perfetto.perfetto_tool import PerfettoConfig, PerfettoTool
+    from .global_config import get_preferences
+    from .targets import load_target
+    from .targets_ops import TargetExecError, exec_on_target_sync, get_target_ssh_info
 
-    config = PerfettoConfig(
-        workspace_root=".",
-        storage_dir=str(Path.home() / ".wafer" / "perfetto"),
-    )
-    tool = PerfettoTool(config)
+    # Determine verbosity
+    prefs = get_preferences()
+    if quiet:
+        show_status = False
+    elif verbose:
+        show_status = True
+    else:
+        show_status = prefs.mode == "explicit"
 
+    # Load target
     try:
-        results, err = tool.query(sql, str(trace_path))
-        if err:
-            typer.echo(f"Error: {err}", err=True)
-            raise typer.Exit(1)
-
-        if json_output:
-            typer.echo(json.dumps({"results": results, "count": len(results or [])}, indent=2))
-        else:
-            if not results:
-                typer.echo("No results")
-            else:
-                # Simple table output
-                if results:
-                    headers = list(results[0].keys())
-                    typer.echo("\t".join(headers))
-                    for row in results:
-                        typer.echo("\t".join(str(row.get(h, "")) for h in headers))
-    except Exception as e:
+        target_config = load_target(target)
+    except FileNotFoundError as e:
+        typer.echo(f"Error: {e}", err=True)
+        typer.echo("List available targets with: wafer config targets list", err=True)
+        raise typer.Exit(1) from None
+    except ValueError as e:
+        typer.echo(f"Error loading target config: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Target: {target} ({type(target_config).__name__})", err=True)
+
+    # Get SSH info (may provision)
+    if show_status:
+        typer.echo("[wafer] Connecting to target...", err=True)
+
+    try:
+        ssh_info = trio.run(get_target_ssh_info, target_config)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Connected: {ssh_info.user}@{ssh_info.host}:{ssh_info.port}", err=True)
+
+    # Build command string
+    if isinstance(command, list):
+        import shlex
+
+        # Remove leading "--" if present
+        if command and command[0] == "--":
+            command = command[1:]
+
+        if not command:
+            typer.echo("Error: No command specified", err=True)
+            raise typer.Exit(1)
+
+        if len(command) == 1:
+            command_str = command[0]
+        else:
+            command_str = shlex.join(command)
+    else:
+        command_str = command
+
+    # Default timeout
+    effective_timeout = timeout if timeout is not None else 300
+
+    if show_status:
+        typer.echo(f"[wafer] Executing (timeout: {effective_timeout}s)...", err=True)
+
+    # Execute
+    try:
+        exit_code = exec_on_target_sync(ssh_info, command_str, effective_timeout)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Exit code: {exit_code}", err=True)
+
+    raise typer.Exit(exit_code)
+
+
+@targets_ops_app.command("ssh")
+def targets_ssh(
+    target: str = typer.Argument(
+        ...,
+        help="Target name",
+        autocompletion=complete_target_name,
+    ),
+) -> None:
+    """SSH into a configured target.
+
+    Provisions the target if needed (RunPod, DigitalOcean), then starts an interactive SSH session.
+    For cloud targets, the instance is kept alive - use 'wafer config targets cleanup <name>' to terminate.
+
+    Examples:
+        wafer targets ssh runpod-mi300x
+        wafer targets ssh my-baremetal-server
+    """
+    from .targets import load_target
+    from .targets_ops import TargetExecError, get_target_ssh_info
+
+    # Load target
+    try:
+        target_config = load_target(target)
+    except FileNotFoundError as e:
+        typer.echo(f"Error: {e}", err=True)
+        typer.echo("List available targets with: wafer config targets list", err=True)
+        raise typer.Exit(1) from None
+    except ValueError as e:
+        typer.echo(f"Error loading target config: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    typer.echo(f"Connecting to target: {target}...", err=True)
+
+    # Get SSH info (may provision)
+    try:
+        ssh_info = trio.run(get_target_ssh_info, target_config)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    # Build SSH command
+    ssh_args = [
+        "ssh",
+        "-i",
+        str(ssh_info.key_path),
+        "-p",
+        str(ssh_info.port),
+        "-o",
+        "StrictHostKeyChecking=no",
+        "-o",
+        "UserKnownHostsFile=/dev/null",
+        f"{ssh_info.user}@{ssh_info.host}",
+    ]
+
+    # Replace current process with SSH
+    os.execvp("ssh", ssh_args)
+
+
+@targets_ops_app.command("sync")
+def targets_sync(
+    target: str = typer.Argument(
+        ...,
+        help="Target name",
+        autocompletion=complete_target_name,
+    ),
+    path: Path = typer.Argument(..., help="Local file or directory to sync"),
+    dest: str | None = typer.Option(
+        None,
+        "--dest",
+        "-d",
+        help="Remote destination path (default: /tmp/<basename>)",
+    ),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show [wafer] status messages"),
+    quiet: bool = typer.Option(False, "--quiet", "-q", help="Suppress [wafer] status messages"),
+) -> None:
+    """Sync local files to a configured target.
+
+    Uses rsync over SSH to copy files to the target. Provisions the target if needed.
+
+    Examples:
+        wafer targets sync runpod-mi300x ./my-project
+        wafer targets sync runpod-mi300x ./script.py --dest /workspace/script.py
+        wafer targets sync my-server ./kernels --dest /tmp/kernels
+    """
+    from .global_config import get_preferences
+    from .targets import load_target
+    from .targets_ops import TargetExecError, get_target_ssh_info, sync_to_target
+
+    # Determine verbosity
+    prefs = get_preferences()
+    if quiet:
+        show_status = False
+    elif verbose:
+        show_status = True
+    else:
+        show_status = prefs.mode == "explicit"
+
+    # Validate path
+    if not path.exists():
+        typer.echo(f"Error: Path not found: {path}", err=True)
+        raise typer.Exit(1)
+
+    # Load target
+    try:
+        target_config = load_target(target)
+    except FileNotFoundError as e:
+        typer.echo(f"Error: {e}", err=True)
+        typer.echo("List available targets with: wafer config targets list", err=True)
+        raise typer.Exit(1) from None
+    except ValueError as e:
+        typer.echo(f"Error loading target config: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Target: {target} ({type(target_config).__name__})", err=True)
+
+    # Get SSH info (may provision)
+    if show_status:
+        typer.echo("[wafer] Connecting to target...", err=True)
+
+    try:
+        ssh_info = trio.run(get_target_ssh_info, target_config)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Connected: {ssh_info.user}@{ssh_info.host}:{ssh_info.port}", err=True)
+
+    # Sync
+    def on_progress(msg: str) -> None:
+        if show_status:
+            typer.echo(f"[wafer] {msg}", err=True)
+
+    try:
+        file_count = sync_to_target(ssh_info, path.resolve(), dest, on_progress)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Done. Synced {file_count} files.", err=True)
+
+
+@targets_ops_app.command("scp")
+def targets_scp(
+    source: str = typer.Argument(..., help="Source path (prefix with target: for remote)"),
+    dest: str = typer.Argument(..., help="Destination path (prefix with target: for remote)"),
+    recursive: bool = typer.Option(False, "-r", "--recursive", help="Copy directories recursively"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show [wafer] status messages"),
+    quiet: bool = typer.Option(False, "--quiet", "-q", help="Suppress [wafer] status messages"),
+) -> None:
+    """Copy files to/from a target using scp-style syntax.
+
+    Use target: prefix to indicate remote paths. Exactly one of source or dest
+    must be remote.
+
+    Examples:
+        wafer targets scp runpod-mi300x:/tmp/trace.json ./trace.json  # download
+        wafer targets scp ./script.py runpod-mi300x:/tmp/script.py    # upload
+        wafer targets scp -r ./kernels runpod-mi300x:/tmp/kernels     # upload dir
+        wafer targets scp -r runpod-mi300x:/tmp/results ./results     # download dir
+    """
+    from .global_config import get_preferences
+    from .targets import load_target
+    from .targets_ops import TargetExecError, get_target_ssh_info, parse_scp_path, scp_transfer
+
+    # Determine verbosity
+    prefs = get_preferences()
+    if quiet:
+        show_status = False
+    elif verbose:
+        show_status = True
+    else:
+        show_status = prefs.mode == "explicit"
+
+    # Parse source and dest
+    source_target, source_path = parse_scp_path(source)
+    dest_target, dest_path = parse_scp_path(dest)
+
+    # Validate: exactly one must be remote
+    if source_target and dest_target:
+        typer.echo("Error: Both paths are remote. Use ssh to transfer between remotes.", err=True)
+        raise typer.Exit(1)
+
+    if not source_target and not dest_target:
+        typer.echo("Error: Both paths are local. Use regular cp command.", err=True)
+        raise typer.Exit(1)
+
+    # Determine direction and target
+    is_download = source_target is not None
+    target_name = source_target if is_download else dest_target
+
+    # Load target
+    try:
+        target_config = load_target(target_name)
+    except FileNotFoundError:
+        typer.echo(f"Error: Target '{target_name}' not found.", err=True)
+        typer.echo("Run 'wafer config targets list' to see available targets.", err=True)
+        raise typer.Exit(1) from None
+    except ValueError as e:
+        typer.echo(f"Error loading target config: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    # Validate local path exists (for upload)
+    if not is_download:
+        local_path = Path(source_path)
+        if not local_path.exists():
+            typer.echo(f"Error: Local path '{source_path}' does not exist.", err=True)
+            raise typer.Exit(1)
+        if local_path.is_dir() and not recursive:
+            typer.echo(
+                f"Error: '{source_path}' is a directory. Use -r flag for recursive copy.", err=True
+            )
+            raise typer.Exit(1)
+
+    if show_status:
+        typer.echo(f"[wafer] Target: {target_name} ({type(target_config).__name__})", err=True)
+        typer.echo("[wafer] Connecting to target...", err=True)
+
+    # Get SSH info (may provision)
+    try:
+        ssh_info = trio.run(get_target_ssh_info, target_config)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Connected: {ssh_info.user}@{ssh_info.host}:{ssh_info.port}", err=True)
+        direction = "Downloading" if is_download else "Uploading"
+        typer.echo(f"[wafer] {direction}...", err=True)
+
+    # Transfer
+    try:
+        if is_download:
+            scp_transfer(ssh_info, source_path, dest_path, is_download=True, recursive=recursive)
+        else:
+            scp_transfer(ssh_info, source_path, dest_path, is_download=False, recursive=recursive)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo("[wafer] Done.", err=True)
+
+
+@targets_ops_app.command("ensure")
+def targets_ensure(  # noqa: PLR0915
+    target: str = typer.Argument(
+        None,
+        help="Target name",
+        autocompletion=complete_target_name,
+    ),
+    tool: str = typer.Argument(None, help="Tool to ensure is installed"),
+    check_only: bool = typer.Option(False, "--check-only", "-c", help="Only check, don't install"),
+    force: bool = typer.Option(False, "--force", "-f", help="Reinstall even if present"),
+    list_tools: bool = typer.Option(False, "--list", "-l", help="List available tools"),
+    timeout: int = typer.Option(300, "--timeout", "-t", help="Installation timeout in seconds"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show [wafer] status messages"),
+    quiet: bool = typer.Option(False, "--quiet", "-q", help="Suppress [wafer] status messages"),
+) -> None:
+    """Ensure a tool is installed on a target.
+
+    Checks if a tool exists on the target and installs it if missing.
+    Useful for profiling tools like rocprof-compute that aren't pre-installed.
+
+    Examples:
+        wafer targets ensure runpod-mi300x rocprof-compute
+        wafer targets ensure runpod-mi300x rocprof-compute --check-only
+        wafer targets ensure runpod-mi300x rocprof-compute --force
+        wafer targets ensure --list
+    """
+    from .global_config import get_preferences
+    from .targets import load_target
+    from .targets_ops import (
+        TOOL_REGISTRY,
+        TargetExecError,
+        ensure_tool,
+        get_target_platform,
+        get_target_ssh_info,
+    )
+
+    # Handle --list flag
+    if list_tools:
+        typer.echo("Available tools:\n")
+        typer.echo("AMD tools:")
+        for name, spec in sorted(TOOL_REGISTRY.items()):
+            if spec.platform == "amd":
+                auto = "auto-install" if spec.install_cmd else "manual"
+                typer.echo(f"  {name:20} ({auto}) - {spec.description}")
+
+        typer.echo("\nNVIDIA tools:")
+        for name, spec in sorted(TOOL_REGISTRY.items()):
+            if spec.platform == "nvidia":
+                auto = "auto-install" if spec.install_cmd else "manual"
+                typer.echo(f"  {name:20} ({auto}) - {spec.description}")
+
+        typer.echo("\nCross-platform:")
+        for name, spec in sorted(TOOL_REGISTRY.items()):
+            if spec.platform == "any":
+                auto = "auto-install" if spec.install_cmd else "manual"
+                typer.echo(f"  {name:20} ({auto}) - {spec.description}")
+        return
+
+    # Require target and tool if not listing
+    if not target:
+        typer.echo("Error: Missing argument 'TARGET'", err=True)
+        typer.echo("Usage: wafer targets ensure TARGET TOOL", err=True)
+        typer.echo("   or: wafer targets ensure --list", err=True)
+        raise typer.Exit(1)
+
+    if not tool:
+        typer.echo("Error: Missing argument 'TOOL'", err=True)
+        typer.echo("Usage: wafer targets ensure TARGET TOOL", err=True)
+        typer.echo("   or: wafer targets ensure --list", err=True)
+        raise typer.Exit(1)
+
+    # Check tool exists
+    if tool not in TOOL_REGISTRY:
+        typer.echo(f"Error: Unknown tool '{tool}'", err=True)
+        typer.echo(f"Available tools: {', '.join(sorted(TOOL_REGISTRY.keys()))}", err=True)
+        typer.echo("Run 'wafer targets ensure --list' for details.", err=True)
+        raise typer.Exit(1)
+
+    spec = TOOL_REGISTRY[tool]
+
+    # Determine verbosity
+    prefs = get_preferences()
+    if quiet:
+        show_status = False
+    elif verbose:
+        show_status = True
+    else:
+        show_status = prefs.mode == "explicit"
+
+    # Load target
+    try:
+        target_config = load_target(target)
+    except FileNotFoundError as e:
+        typer.echo(f"Error: {e}", err=True)
+        typer.echo("List available targets with: wafer config targets list", err=True)
+        raise typer.Exit(1) from None
+    except ValueError as e:
+        typer.echo(f"Error loading target config: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    # Platform validation
+    platform = get_target_platform(target_config)
+    if spec.platform != "any" and spec.platform != platform:
+        typer.echo(
+            f"Error: {tool} is an {spec.platform.upper()} tool but target '{target}' "
+            f"is {platform.upper()}",
+            err=True,
+        )
+        raise typer.Exit(1)
+
+    if show_status:
+        typer.echo(f"[wafer] Target: {target} ({platform.upper()})", err=True)
+        typer.echo(f"[wafer] Checking for {tool}...", err=True)
+
+    # Get SSH info (may provision)
+    try:
+        ssh_info = trio.run(get_target_ssh_info, target_config)
+    except TargetExecError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1) from None
+
+    if show_status:
+        typer.echo(f"[wafer] Connected: {ssh_info.user}@{ssh_info.host}:{ssh_info.port}", err=True)
+
+    # Check-only mode
+    if check_only:
+        from .targets_ops import TargetExecError, exec_on_target_sync
+
+        try:
+            exit_code = exec_on_target_sync(ssh_info, spec.check_cmd, timeout_seconds=30)
+        except TargetExecError as e:
+            typer.echo(f"Error: {e}", err=True)
+            raise typer.Exit(1) from None
+        if exit_code == 0:
+            typer.echo(f"{tool} is installed")
+        else:
+            typer.echo(f"{tool} is NOT installed", err=True)
+            raise typer.Exit(1)
+        return
+
+    # Ensure tool is installed
+    result = ensure_tool(ssh_info, tool, force=force, timeout=timeout)
+
+    if result.error:
+        typer.echo(f"Error: {result.error}", err=True)
+        raise typer.Exit(1)
+
+    if result.already_installed:
+        typer.echo(f"{tool} is already installed")
+    elif result.installed:
+        if result.verified:
+            typer.echo(f"{tool} installed successfully")
+        else:
+            typer.echo(f"{tool} installed (verification skipped)")
+
+
+# =============================================================================
+# Perfetto trace analysis commands
+# =============================================================================
+
+
+@perfetto_app.command("query")
+def perfetto_query(
+    trace_path: Path = typer.Argument(..., help="Path to Perfetto trace file"),
+    sql: str = typer.Argument(..., help="SQL query to execute"),
+    json_output: bool = typer.Option(True, "--json", "-j", help="Output as JSON"),
+) -> None:
+    """Execute SQL query against a Perfetto trace.
+
+    Starts trace_processor, loads the trace, executes the query, and returns results.
+
+    Examples:
+        wafer perfetto query trace.perfetto "SELECT * FROM slice LIMIT 10"
+        wafer perfetto query trace.perfetto "SELECT name, dur FROM slice ORDER BY dur DESC LIMIT 5"
+    """
+    from wafer_core.lib.perfetto.perfetto_tool import PerfettoConfig, PerfettoTool
+
+    config = PerfettoConfig(
+        workspace_root=".",
+        storage_dir=str(Path.home() / ".wafer" / "perfetto"),
+    )
+    tool = PerfettoTool(config)
+
+    try:
+        results, err = tool.query(sql, str(trace_path))
+        if err:
+            typer.echo(f"Error: {err}", err=True)
+            raise typer.Exit(1)
+
+        if json_output:
+            typer.echo(json.dumps({"results": results, "count": len(results or [])}, indent=2))
+        else:
+            if not results:
+                typer.echo("No results")
+            else:
+                # Simple table output
+                if results:
+                    headers = list(results[0].keys())
+                    typer.echo("\t".join(headers))
+                    for row in results:
+                        typer.echo("\t".join(str(row.get(h, "")) for h in headers))
+    except Exception as e:
         typer.echo(f"Error: {e}", err=True)
         raise typer.Exit(1) from None
 
@@ -4774,13 +5533,39 @@ def ncu_analyze(
 
 
 # =============================================================================
-# NSYS Analyze command
+# NSYS commands
 # =============================================================================
 
 
+@nsys_app.command("check")
+def nsys_check() -> None:
+    """Check if NSYS (Nsight Systems) is installed and show version.
+
+    NSYS is required for local analysis. If not installed, shows install instructions.
+
+    Examples:
+        wafer nvidia nsys check
+    """
+    from .nsys_analyze import check_nsys_installation
+
+    result = check_nsys_installation()
+
+    if result.installed:
+        typer.echo(f"✓ NSYS installed: {result.path}")
+        if result.version:
+            typer.echo(f"  Version: {result.version}")
+    else:
+        typer.echo("✗ NSYS not installed")
+        if result.install_command:
+            typer.echo(f"  Install with: {result.install_command}")
+
+
 @nsys_app.command("analyze")
 def nsys_analyze(
     filepath: Path = typer.Argument(..., help="Path to .nsys-rep profile file"),
+    output_dir: Path | None = typer.Option(
+        None, "--output-dir", "-o", help="Output directory for analysis files"
+    ),
     json_output: bool = typer.Option(
         False, "--json", help="Output raw JSON instead of formatted text"
     ),
@@ -4789,6 +5574,12 @@ def nsys_analyze(
         "--remote/--local",
         help="Force remote (via API) or local analysis. Default: auto-detect (remote if nsys not installed locally)",
     ),
+    target: str | None = typer.Option(
+        None,
+        "--target",
+        "-t",
+        help="Remote target: 'workspace:id' for workspace execution, or target name from ~/.wafer/targets/",
+    ),
 ) -> None:
     """Analyze an NVIDIA Nsight Systems profile (.nsys-rep file).
 
@@ -4797,10 +5588,20 @@ def nsys_analyze(
     By default, uses local nsys if available, otherwise runs analysis
     remotely via wafer-api (requires authentication: wafer login).
 
+    Supports multiple execution modes:
+    - Local: Uses local nsys CLI (no GPU required for analysis)
+    - Remote API: Uploads file and runs analysis on Modal
+    - Workspace: Runs analysis on a Wafer workspace via SSH
+    - Target: Runs analysis on a configured target machine via SSH
+
     Examples:
         wafer nvidia nsys analyze profile.nsys-rep
         wafer nvidia nsys analyze profile.nsys-rep --json
+        wafer nvidia nsys analyze profile.nsys-rep --local
         wafer nvidia nsys analyze profile.nsys-rep --remote
+        wafer nvidia nsys analyze profile.nsys-rep --target workspace:abc123
+        wafer nvidia nsys analyze profile.nsys-rep --target vultr-b200
+        wafer nvidia nsys analyze profile.nsys-rep -o ./results/
     """
     from .nsys_analyze import analyze_nsys_profile
 
@@ -4812,11 +5613,20 @@ def nsys_analyze(
         typer.echo(f"Error: Expected .nsys-rep file, got: {filepath.suffix}", err=True)
         raise typer.Exit(1)
 
+    # Warn if both remote flag and target are specified
+    if target and remote is not None:
+        typer.echo(
+            "Warning: --target overrides --remote/--local flag",
+            err=True,
+        )
+
     try:
         result = analyze_nsys_profile(
             filepath,
             json_output=json_output,
             remote=remote,
+            target=target,
+            output_dir=output_dir,
         )
         typer.echo(result)
     except FileNotFoundError as e:
@@ -4827,6 +5637,150 @@ def nsys_analyze(
         raise typer.Exit(1) from None
 
 
+@nsys_app.command("profile", context_settings={"allow_interspersed_args": False})
+def nsys_profile(
+    command: list[str] = typer.Argument(..., help="Command to profile"),
+    output: str = typer.Option(
+        "profile",
+        "--output",
+        "-o",
+        help="Output filename (without .nsys-rep extension)",
+    ),
+    trace: str | None = typer.Option(
+        None,
+        "--trace",
+        "-t",
+        help="Trace APIs to capture (comma-separated: cuda,nvtx,osrt,cudnn,cublas). Default: cuda",
+    ),
+    duration: int | None = typer.Option(
+        None,
+        "--duration",
+        "-d",
+        help="Maximum profiling duration in seconds",
+    ),
+    target: str | None = typer.Option(
+        None,
+        "--target",
+        help="Remote target: 'workspace:id' for workspace execution, or target name from ~/.wafer/targets/",
+    ),
+    analyze: bool = typer.Option(
+        False,
+        "--analyze",
+        "-a",
+        help="Automatically analyze the profile after completion",
+    ),
+    json_output: bool = typer.Option(
+        False,
+        "--json",
+        help="Output analysis as JSON (only with --analyze)",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "--verbose",
+        "-v",
+        help="Show verbose progress messages",
+    ),
+    extra_args: str | None = typer.Option(
+        None,
+        "--extra",
+        help="Extra arguments to pass to nsys profile",
+    ),
+) -> None:
+    """Profile a command with NVIDIA Nsight Systems.
+
+    Runs nsys profile on the specified command and generates a .nsys-rep file.
+    Profiling requires an NVIDIA GPU. Use --target to run on a remote GPU server
+    or workspace.
+
+    Examples:
+        wafer nvidia nsys profile -- python train.py
+        wafer nvidia nsys profile -o gemm_profile -- ./gemm_kernel
+        wafer nvidia nsys profile --trace cuda,nvtx -- python model.py
+        wafer nvidia nsys profile --duration 60 -- ./long_running_app
+        wafer nvidia nsys profile --target workspace:abc123 -- python test.py
+        wafer nvidia nsys profile --target vultr-b200 -- ./benchmark
+        wafer nvidia nsys profile --analyze -- python train.py
+        wafer nvidia nsys profile --analyze --json -- ./kernel > results.json
+    """
+    # Parse command
+    import shlex
+
+    from .nsys_analyze import _parse_target
+    from .nsys_profile import (
+        NSYSProfileOptions,
+        profile_and_analyze,
+        profile_local,
+        profile_remote_ssh,
+        profile_workspace,
+    )
+
+    if isinstance(command, list):
+        # Remove leading "--" if present
+        if command and command[0] == "--":
+            command = command[1:]
+        if len(command) == 1:
+            command_str = command[0]
+        else:
+            command_str = shlex.join(command)
+    else:
+        command_str = command
+
+    if not command_str:
+        typer.echo("Error: No command specified", err=True)
+        raise typer.Exit(1)
+
+    # Parse trace options
+    trace_list = trace.split(",") if trace else None
+
+    # Build options
+    options = NSYSProfileOptions(
+        command=command_str,
+        output=output,
+        trace=trace_list,
+        duration=duration,
+        extra_args=extra_args,
+    )
+
+    if verbose:
+        typer.echo(f"[nsys] Command: {command_str}", err=True)
+        if target:
+            typer.echo(f"[nsys] Target: {target}", err=True)
+
+    # Execute
+    if analyze:
+        profile_result, analysis_result = profile_and_analyze(
+            options,
+            target=target,
+            json_output=json_output,
+            verbose=verbose,
+        )
+    else:
+        if target:
+            target_type, target_id = _parse_target(target)
+            if target_type == "workspace":
+                profile_result = profile_workspace(target_id, options, verbose=verbose)
+            else:
+                profile_result = profile_remote_ssh(target_id, options, verbose=verbose)
+        else:
+            profile_result = profile_local(options, verbose=verbose)
+        analysis_result = None
+
+    # Report results
+    if not profile_result.success:
+        typer.echo(f"Error: {profile_result.error}", err=True)
+        if profile_result.stderr:
+            typer.echo(f"stderr: {profile_result.stderr}", err=True)
+        raise typer.Exit(1)
+
+    if verbose or not analyze:
+        typer.echo(f"Profile created: {profile_result.output_path}")
+
+    if analysis_result:
+        if not analysis_result.success:
+            typer.echo(f"Analysis error: {analysis_result.error}", err=True)
+            raise typer.Exit(1)
+
+
 # =============================================================================
 # ROCprof-Compute commands
 # =============================================================================
@@ -5959,13 +6913,14 @@ def capture_list_command(
 
 @corpus_app.command("download")
 def corpus_download(
-    name: str = typer.Argument(..., help="Corpus name (cuda, cutlass, hip)"),
+    name: str = typer.Argument(..., help="Corpus name (cuda, cutlass, hip, amd)"),
     force: bool = typer.Option(False, "--force", "-f", help="Re-download even if exists"),
 ) -> None:
     """Download a documentation corpus for agent filesystem access.
 
     Examples:
         wafer corpus download cuda
+        wafer corpus download amd
         wafer corpus download cutlass --force
     """
     from .corpus import CORPORA, download_corpus
@@ -6180,78 +7135,12 @@ def tracelens_collective(
 
 
 # =============================================================================
-# ISA Analysis Commands
+# Unified ISA Analysis Commands (wafer amd isa ...)
 # =============================================================================
 
 
 @isa_app.command("analyze")
 def isa_analyze(
-    file: Path = typer.Argument(..., help="Path to .co file to analyze"),
-    json_output: bool = typer.Option(False, "--json", help="Output as JSON"),
-) -> None:
-    """Analyze AMD GPU code object (.co file).
-
-    Extracts and analyzes ISA, showing register usage, instruction mix,
-    spills, and other performance-relevant metrics.
-
-    The .co file is uploaded to the Wafer API server which has ROCm tools
-    installed for analysis.
-
-    Examples:
-        wafer isa analyze kernel.co
-        wafer isa analyze kernel.co --json
-    """
-    from dataclasses import asdict
-
-    from wafer_core.tools.isa_analysis_tools import analyze_isa, format_isa_summary
-
-    from .auth import get_auth_headers
-    from .global_config import get_api_url
-
-    # Validate file exists
-    if not file.exists():
-        typer.echo(f"Error: File not found: {file}", err=True)
-        raise typer.Exit(1)
-
-    if not file.suffix == ".co":
-        typer.echo(f"Error: Expected .co file, got: {file.suffix}", err=True)
-        raise typer.Exit(1)
-
-    # Get API URL and auth
-    api_url = get_api_url()
-    auth_headers = get_auth_headers()
-
-    if not auth_headers:
-        typer.echo("Error: Not logged in. Run 'wafer login' first.", err=True)
-        raise typer.Exit(1)
-
-    try:
-        result = analyze_isa(
-            co_file_path=file,
-            api_url=api_url,
-            auth_headers=auth_headers,
-        )
-
-        if json_output:
-            typer.echo(json.dumps(asdict(result)))
-        else:
-            typer.echo(format_isa_summary(result))
-
-    except FileNotFoundError as e:
-        typer.echo(f"Error: {e}", err=True)
-        raise typer.Exit(1) from None
-    except Exception as e:
-        typer.echo(f"Error: {e}", err=True)
-        raise typer.Exit(1) from None
-
-
-# =============================================================================
-# Kernel Scope Commands (wafer amd kernel-scope ...)
-# =============================================================================
-
-
-@kernel_scope_app.command("analyze")
-def kernel_scope_analyze(
     path: Path = typer.Argument(..., help="Path to file or directory to analyze"),
     json_output: bool = typer.Option(False, "--json", "-j", help="Output as JSON"),
     csv_output: bool = typer.Option(False, "--csv", help="Output as CSV"),
@@ -6264,24 +7153,32 @@ def kernel_scope_analyze(
     output_file: Path | None = typer.Option(None, "--output", "-o", help="Write output to file"),
     kernel_index: int = typer.Option(0, "--kernel", "-k", help="Kernel index if multiple in file"),
 ) -> None:
-    """Analyze Triton compilation artifacts (ISA, LLVM-IR, TTGIR).
+    """Analyze AMD GPU ISA files (.co, .s, .ll, .ttgir).
 
     Performs static analysis to extract performance metrics like register
     pressure, spills, MFMA density, and occupancy limits.
 
     Supports:
-      - AMDGCN ISA files (.s, .gcn, .asm)
-      - LLVM-IR files (.ll)
-      - TTGIR files (.ttgir, .ttir, .mlir)
+      - AMD GPU code objects (.co) - Requires API authentication
+      - AMDGCN ISA assembly (.s, .gcn, .asm) - Local parsing
+      - LLVM-IR files (.ll) - Local parsing
+      - TTGIR files (.ttgir, .ttir, .mlir) - Local parsing
 
     Examples:
-        wafer amd kernel-scope analyze kernel.s
-        wafer amd kernel-scope analyze kernel.s --json
-        wafer amd kernel-scope analyze ~/.triton/cache/ --filter 'spills > 0'
-        wafer amd kernel-scope analyze . -r --csv -o metrics.csv
+        wafer amd isa analyze kernel.co              # Code object (needs login)
+        wafer amd isa analyze kernel.s               # ISA assembly
+        wafer amd isa analyze kernel.s --json        # Output as JSON
+        wafer amd isa analyze ~/.triton/cache/ --filter 'spills > 0'
+        wafer amd isa analyze . -r --csv -o metrics.csv
     """
+    from .auth import get_auth_headers
+    from .global_config import get_api_url
     from .kernel_scope import analyze_command
 
+    # Get API credentials for .co files
+    api_url = get_api_url()
+    auth_headers = get_auth_headers()
+
     try:
         output = analyze_command(
             path=str(path),
@@ -6291,6 +7188,8 @@ def kernel_scope_analyze(
             filter_expr=filter_expr,
             output_file=str(output_file) if output_file else None,
             kernel_index=kernel_index,
+            api_url=api_url,
+            auth_headers=auth_headers,
         )
         typer.echo(output)
 
@@ -6305,15 +7204,15 @@ def kernel_scope_analyze(
         raise typer.Exit(1) from None
 
 
-@kernel_scope_app.command("metrics")
-def kernel_scope_metrics() -> None:
-    """List available metrics for kernel scope analysis.
+@isa_app.command("metrics")
+def isa_metrics() -> None:
+    """List available metrics for ISA analysis.
 
-    Shows all metrics that can be extracted from Triton compilation
-    artifacts, along with their derivation.
+    Shows all metrics that can be extracted from AMD GPU ISA files,
+    along with their derivation.
 
     Examples:
-        wafer amd kernel-scope metrics
+        wafer amd isa metrics
     """
     from .kernel_scope import metrics_command
 
@@ -6321,15 +7220,15 @@ def kernel_scope_metrics() -> None:
     typer.echo(output)
 
 
-@kernel_scope_app.command("targets")
-def kernel_scope_targets() -> None:
+@isa_app.command("targets")
+def isa_targets() -> None:
     """List supported GPU targets and their specifications.
 
     Shows hardware specs (VGPRs, SGPRs, LDS, etc.) for each supported
     AMD GPU architecture.
 
     Examples:
-        wafer amd kernel-scope targets
+        wafer amd isa targets
     """
     from .kernel_scope import targets_command