fix: treat --apply/--contain as flags, not user text

AGENTS.md

@@ -35,7 +35,7 @@ src/
     initializeProject.ts Initialize Project command: generate/diff AGENTS.md
     managedInstall.ts    Managed Install commands: install, update, reinstall Patchloom binary
     quickActions.ts       Quick Action command: replace, tidy, doc set, search, create, append, prepend, doc get, patch merge
-    batchApply.ts        Batch Apply command: atomic multi-operation plan via JSON
+    batchApply.ts        Batch Apply command: atomic multi-operation plan (line-oriented, not JSON)
     setupWorkspace.ts     Setup Workspace command: guided readiness walkthrough
     showStatus.ts         Show Status command: diagnostics display
     verifyMcp.ts         Verify MCP Server command: JSON-RPC initialize probe
@@ -85,7 +85,7 @@ scripts/
   actions/
     setup-node/            Composite: Node.js from .nvmrc + npm ci
   workflows/
-    ci.yml                 CI: unit tests, build, integration tests (self-hosted)
+    ci.yml                 CI: unit tests, build, integration tests (GitHub-hosted matrix)
     auto-approve.yml           Auto-approve PRs from SebTardif and dependabot[bot]
     dependabot-auto-merge.yml  Auto-merge minor/patch Dependabot PRs
     dco.yml                    DCO sign-off check on PRs

ROADMAP.md

@@ -2,16 +2,13 @@
 
 This roadmap reflects current priorities. It is not a commitment and may change based on community feedback.
 
-## Near-term
+## Shipped
 
-- **Marketplace publish** ([#2](https://github.com/patchloom/patchloom-vscode/issues/2)): Publish to the VS Code Marketplace and Open VSX so users can install directly from the editor.
-- **Cross-platform CI** ([#25](https://github.com/patchloom/patchloom-vscode/issues/25)): Add Linux and Windows to the unit test matrix now that the repo is public and GitHub-hosted runners are available.
-- **Branch protection and Dependabot auto-merge** ([#43](https://github.com/patchloom/patchloom-vscode/issues/43)): Enable branch protection on `main` and unblock Dependabot auto-merge.
-
-## Medium-term
-
-- **Cross-platform integration tests** ([#39](https://github.com/patchloom/patchloom-vscode/issues/39)): Extend extension and UI tests to Linux and Windows.
-- **Managed binary install** ([#9](https://github.com/patchloom/patchloom-vscode/issues/9)): Automatically download and manage the Patchloom CLI binary. Blocked on the CLI publishing platform-specific archives.
+- **Marketplace publish** ([#2](https://github.com/patchloom/patchloom-vscode/issues/2)): VS Code Marketplace and Open VSX.
+- **Cross-platform CI** ([#25](https://github.com/patchloom/patchloom-vscode/issues/25)): Linux, macOS, and Windows unit and integration tests on GitHub-hosted runners.
+- **Branch protection and Dependabot auto-merge** ([#43](https://github.com/patchloom/patchloom-vscode/issues/43)): Ruleset on `main` plus Dependabot auto-merge for patch/minor updates.
+- **Cross-platform integration tests** ([#39](https://github.com/patchloom/patchloom-vscode/issues/39)): Extension and UI tests on Linux, macOS, and Windows.
+- **Managed binary install** ([#9](https://github.com/patchloom/patchloom-vscode/issues/9)): Download, verify, extract, and promote the Patchloom CLI.
 
 ## Long-term
 

src/commands/quickActions.ts

@@ -1536,17 +1536,15 @@ export function retargetQuickAction(action: PlannedQuickAction, nextTargetPath:
 }
 
 export function withApplyFlag(args: readonly string[]): string[] {
-  return args.includes("--apply") ? [...args] : [...args, "--apply"];
+  return args.at(-1) === "--apply" ? [...args] : [...args, "--apply"];
 }
 
 /**
  * Prepend the global `--contain` flag so CLI ops cannot escape the cwd workspace.
  * Global flags must appear before the subcommand (`patchloom --contain replace ...`).
  */
 export function withContainFlag(args: readonly string[]): string[] {
-  return args[0] === "--contain" || args.includes("--contain")
-    ? [...args]
-    : ["--contain", ...args];
+  return args[0] === "--contain" ? [...args] : ["--contain", ...args];
 }
 
 async function previewAndMaybeApply(

test/unit/quickActions.test.ts

@@ -267,6 +267,12 @@ test("withApplyFlag appends apply once", () => {
   ]);
 });
 
+test("withApplyFlag still appends when user text is --apply", () => {
+  assert.deepEqual(withApplyFlag(["replace", "--apply", "--new", "x", "f.txt"]), [
+    "replace", "--apply", "--new", "x", "f.txt", "--apply"
+  ]);
+});
+
 test("withContainFlag prefixes global --contain once", () => {
   assert.deepEqual(withContainFlag(["replace", "old", "--new", "new", "f.txt"]), [
     "--contain",
@@ -282,6 +288,7 @@ test("withContainFlag prefixes global --contain once", () => {
     "--apply"
   ]);
   assert.deepEqual(withContainFlag(["doc", "set", "a.json", "port", "1", "--contain"]), [
+    "--contain",
     "doc",
     "set",
     "a.json",
@@ -291,6 +298,12 @@ test("withContainFlag prefixes global --contain once", () => {
   ]);
 });
 
+test("withContainFlag still prefixes when user text is --contain", () => {
+  assert.deepEqual(withContainFlag(["replace", "--contain", "--new", "x", "f.txt"]), [
+    "--contain", "replace", "--contain", "--new", "x", "f.txt"
+  ]);
+});
+
 test("buildPrependQuickAction builds a file prepend command", () => {
   const action = buildPrependQuickAction("/workspace/demo/src/main.ts", "// copyright\n");
   assert.equal(action.title, "Prepend to main.ts");

walkthrough/configure-mcp.md

@@ -9,13 +9,13 @@ for your editor. Choose the **full** tool inventory or the **core** pack
 
 ## Supported Editors
 
-| Editor | Config file |
-|--------|------------|
-| VS Code | `.vscode/mcp.json` |
-| Cursor | `.cursor/mcp.json` |
-| Windsurf | `~/.codeium/windsurf/mcp_config.json` |
+| Editor | Config file | Key |
+|--------|-------------|-----|
+| VS Code | `.vscode/mcp.json` | `servers` |
+| Cursor | `.cursor/mcp.json` | `mcpServers` |
+| Windsurf | `~/.codeium/windsurf/mcp_config.json` | `mcpServers` |
 
-The command detects which editors are available and configures them
-automatically.
+The command lists the editors it can configure. You pick one or more
+targets, then Full vs Core. It does not write every editor on its own.
 
 See the [MCP setup guide](https://patchloom.github.io/patchloom/getting-started/mcp-setup.html) for advanced configuration.