feat: align extension with patchloom CLI 0.31.0

AGENTS.md

@@ -51,13 +51,13 @@ test/
     batchApply.test.ts   Batch template and operation count parsing (16 tests)
     binary.test.ts       Binary discovery, managed install, compatibility, workspace env (66 tests)
     binaryDiscovery.test.ts  Real executable discovery on PATH (13 tests)
-    initializeProject.test.ts  Status display, agents file classification, formatError (39 tests)
+    initializeProject.test.ts  Status display, agents file classification, formatError (41 tests)
     managedLifecycle.test.ts   Managed install with real file I/O (22 tests)
     mcpConfig.test.ts    MCP config with real temp directories (12 tests)
     outputChannel.test.ts Output channel logging wrapper (10 tests)
     patchloomCli.test.ts Patchloom CLI integration with real binary + managed install e2e MCP (40 tests incl. e2e)
     propertyBased.test.ts  Property-based tests with fast-check (13 tests)
-    quickActions.test.ts Quick action command building, path containment, patch merge (60 tests)
+    quickActions.test.ts Quick action command building, path containment, patch merge (62 tests)
     verifyMcp.test.ts    MCP server verify and JSON-RPC response parsing (15 tests)
     downloadIntegration.test.ts  HTTP download, redirect, streaming SHA-256 (9 tests)
   suite/

README.md

@@ -53,7 +53,7 @@ Run `Patchloom: Setup Workspace` to walk through everything your project needs:
 
 ### Agent rules generation
 
-`Patchloom: Initialize Project` generates an `AGENTS.md` file from `patchloom agent-rules`. You pick integration mode (CLI/MCP/all), shell platform, and surface (`full` document or `core` pack for system-prompt injection, CLI 0.24+). If `AGENTS.md` already exists, the extension opens a diff so you can merge updates manually.
+`Patchloom: Initialize Project` generates an `AGENTS.md` file from `patchloom agent-rules`. You pick integration mode (CLI/MCP/all), shell platform, and surface (`full` document or `core` pack for system-prompt injection, CLI 0.24+). On CLI 0.29+, `--surface core` honors `--mode` the same way the full surface does. If `AGENTS.md` already exists, the extension opens a diff so you can merge updates manually.
 
 ### MCP server configuration
 
@@ -65,7 +65,7 @@ Run `Patchloom: Setup Workspace` to walk through everything your project needs:
 
 When configuring, pick **Full tool inventory** (default) or **Core pack**. Core sets `PATCHLOOM_MCP_SURFACE=core` on the server entry.
 
-CLI **0.28.0** (and 0.24+) exposes **58** MCP tools by default (including `list_files` and `apply_fragment`). The core pack is 11 tools: `read_file`, `search_files`, `list_files`, `replace_text`, `batch_replace`, `doc_get`, `doc_set`, `doc_query`, `md_replace_section`, `execute_plan`, `server_info`. Absolute paths that resolve inside the MCP workspace root are allowed; empty paths, `../`, and outside paths still reject with stable `error_kind` peels.
+CLI **0.31.0** (and 0.24+) exposes **58** MCP tools by default (including `list_files` and `apply_fragment`). The core pack is 11 tools: `read_file`, `search_files`, `list_files`, `replace_text`, `batch_replace`, `doc_get`, `doc_set`, `doc_query`, `md_replace_section`, `execute_plan`, `server_info`. `search_files` accepts `files_without_match` (CLI 0.29+). `apply_patch` accepts unified diffs, Codex `*** Begin Patch`, and Aider SEARCH/REPLACE (CLI 0.30+). Absolute paths that resolve inside the MCP workspace root are allowed; empty paths, `../`, and outside paths still reject with stable `error_kind` peels.
 
 ### Status bar
 
@@ -94,6 +94,7 @@ Click it to see full diagnostics, including per-editor MCP configuration status
 | **Tidy file** | Whitespace and newline cleanup with diff preview |
 | **Set structured value** | Update a JSON, YAML, or TOML key with diff preview |
 | **Search text** | Find pattern matches across workspace files (results in output channel) |
+| **Search files without match** | List files that do not contain the pattern (`search -L`, CLI 0.29+) |
 | **Create file** | Scaffold a new file with optional content and open it in the editor |
 | **Append to file** | Append content to an existing file |
 | **Prepend to file** | Prepend content to the start of an existing file (CLI 0.9+) |
@@ -175,7 +176,7 @@ The extension detects outdated CLI builds and warns with upgrade guidance. It re
 Set `patchloom.path` in settings, or add the CLI to your `PATH`.
 
 **CLI compatibility warning / upgrade path**
-The extension requires Patchloom **0.3.0** or newer; **0.28.0** is recommended. Which fix to use depends on how the CLI was resolved (status shows Source):
+The extension requires Patchloom **0.3.0** or newer; **0.31.0** is recommended. Which fix to use depends on how the CLI was resolved (status shows Source):
 
 1. **Source: managed install** → **Patchloom: Update Patchloom** (checksum-verified GitHub release into extension storage)
 2. **Source: PATH** → upgrade that install in place (**Scoop** `scoop update patchloom` on Windows; Homebrew / npm / cargo / the official installer elsewhere). Managed Install will not override a PATH binary.
@@ -189,6 +190,21 @@ Quick Actions and Batch Apply pass `--contain` so paths stay inside the open wor
 **Empty or blank path**
 On CLI 0.28+, empty, whitespace-only, or format-character-only paths fail early with `error_kind: invalid_input` and message `path must not be empty` (they no longer look like workspace-root failures). Prefer a real relative or workspace-absolute path.
 
+**Create or rename parent is not a directory**
+On CLI 0.31+, create and rename check each parent of the destination before staging. A parent that is a regular file (or a dangling / file symlink) reports `error_kind: invalid_input` and `parent path is not a directory`. Create the missing directory first, or pick a destination whose parents are directories.
+
+**Numeric or negated doc selector**
+On CLI 0.30+, selectors accept `!=`, `>`, `>=`, `<`, `<=`, and `[!key]` (for example `servers[port>8000]`). A non-numeric compare reports `error_kind: invalid_input`. Use a number on the right-hand side, or a concrete index path.
+
+**Search files without match**
+On CLI 0.29+, `search -L` / `--files-without-match` lists files that do not contain the pattern. Combining it with `--files-with-matches` or `--count` is `invalid_input`. When every scanned file contains the pattern, the CLI reports `error_kind: no_matches` and the text `no files without matches for 'PATTERN' in SCOPE` (that is not a content miss).
+
+**YAML mapping alias stayed an alias**
+On CLI 0.31+, `doc set` on a mapping that is only `service_a: *shared` writes a merge key plus local fields (`<<: *shared` and your new keys) instead of inlining the whole object. Sequence items (`- *shared`) still expand or stay not-applied.
+
+**Patch apply formats**
+On CLI 0.30+, `patch apply` (and MCP `apply_patch`) accepts unified diffs, Codex `*** Begin Patch`, and Aider SEARCH/REPLACE. Update and SEARCH matches must be unique unless you pass `--replace-all` (SEARCH/REPLACE only). The Quick Action **Merge patch (three-way)** is still `patch merge` for stale unified diffs.
+
 **Batch replace shape**
 Batch lines use `replace PATH OLD NEW` (and optional flags such as `--fuzzy`). Do not paste CLI form `replace OLD --new NEW path` into a batch plan; CLI 0.18+ returns a clear parse error with the PATH OLD NEW hint.
 
@@ -240,7 +256,7 @@ File bugs and feature requests at [patchloom/patchloom-vscode/issues](https://gi
 ## Requirements
 
 - VS Code 1.90 or newer (or compatible editors: Cursor, Windsurf, VSCodium)
-- [Patchloom CLI](https://github.com/patchloom/patchloom) 0.3.0 or newer (**0.28.0+ recommended** for empty-path fail-closed (`path must not be empty`), `suggested_op` on fail-closed doc navigation, `not_regular_file` soft peels, ambiguous markdown headings, `list_files` MCP inventory, `apply-fragment`, full `error_kind` peels (`binary` / `invalid_encoding` / `fuzzy_span_suspicious` / `already_exists` / `guard_rejected` / `ambiguous`), optional `PATCHLOOM_MCP_SURFACE=core` 11-tool pack, multi-doc `doc merge --selector`, line-oriented inserts, batch `replace PATH OLD NEW` hints, 58 MCP tools, and agent-facing JSON envelopes)
+- [Patchloom CLI](https://github.com/patchloom/patchloom) 0.3.0 or newer (**0.31.0+ recommended** for YAML alias-to-merge on `doc set`, create/rename `parent path is not a directory`, numeric selector compares (`servers[port>8000]`), `search -L` / `files_without_match`, Codex Begin Patch and Aider SEARCH/REPLACE on `patch apply`, `agent-rules --surface core` honoring `--mode`, empty-path fail-closed (`path must not be empty`), `suggested_op` on fail-closed doc navigation, `not_regular_file` soft peels, ambiguous markdown headings, `list_files` MCP inventory, `apply-fragment`, full `error_kind` peels (`binary` / `invalid_encoding` / `fuzzy_span_suspicious` / `already_exists` / `guard_rejected` / `ambiguous`), optional `PATCHLOOM_MCP_SURFACE=core` 11-tool pack, multi-doc `doc merge --selector`, line-oriented inserts, batch `replace PATH OLD NEW` hints, 58 MCP tools, and agent-facing JSON envelopes)
 
 ## Contributing
 

src/commands/configureMcp.ts

@@ -47,7 +47,7 @@ export async function configureMcp(): Promise<void> {
     [
       {
         label: "Full tool inventory",
-        description: "Default (58 tools on CLI 0.24+; verified on 0.28)",
+        description: "Default (58 tools on CLI 0.24+; verified on 0.31)",
         surface: "full" as const
       },
       {

src/commands/initializeProject.ts

@@ -62,7 +62,7 @@ export async function initializeProject(): Promise<void> {
       },
       {
         label: "Core pack",
-        description: "Short rules for system-prompt injection (CLI 0.24+ --surface core)",
+        description: "Short rules for system-prompt injection (CLI 0.24+ --surface core; 0.29+ honors --mode)",
         surface: "core" as const
       }
     ],

src/commands/quickActions.ts

@@ -259,8 +259,8 @@ export async function runQuickAction(): Promise<void> {
         }
 
         const selector = await vscode.window.showInputBox({
-          prompt: "Selector path",
-          placeHolder: "scripts.test",
+          prompt: "Selector path (CLI 0.30+ accepts numeric compares such as servers[port>8000])",
+          placeHolder: "scripts.test or servers[port>8000]",
           validateInput: (value) => value.length > 0 ? undefined : "Selector is required."
         });
         if (selector === undefined) {
@@ -325,6 +325,55 @@ export async function runQuickAction(): Promise<void> {
         }
       }
     },
+    {
+      label: "Search files without match",
+      description: "List files that do not contain the pattern (CLI 0.29+ -L)",
+      detail: "Builds `patchloom search <pattern> --files-without-match [--glob <glob>] <workspace>`",
+      run: async () => {
+        const folder = await activeWorkspaceFolder({
+          promptIfMany: true,
+          placeHolder: "Select workspace folder for Patchloom search -L"
+        });
+        if (!folder) {
+          await vscode.window.showWarningMessage("Open a workspace folder before running Patchloom search.");
+          return;
+        }
+
+        const pattern = await vscode.window.showInputBox({
+          prompt: "Pattern that listed files must not contain",
+          placeHolder: "TODO|FIXME",
+          validateInput: (value) => value.length > 0 ? undefined : "Pattern is required."
+        });
+        if (pattern === undefined) {
+          return;
+        }
+
+        const glob = await vscode.window.showInputBox({
+          prompt: "File glob (optional, leave empty for all files)",
+          placeHolder: "*.ts"
+        });
+        if (glob === undefined) {
+          return;
+        }
+
+        const action = buildSearchQuickAction(folder.uri.fsPath, pattern, glob || undefined, {
+          filesWithoutMatch: true
+        });
+        const result = await executePatchloom(binaryPath, action.args, folder.uri.fsPath);
+        const log = getPatchloomLog();
+
+        if (result.exitCode === 3) {
+          await vscode.window.showInformationMessage(`Every scanned file contains "${pattern}".`);
+        } else if (result.exitCode !== 0) {
+          await vscode.window.showErrorMessage(`Patchloom search failed: ${formatCliOutput(result)}`);
+        } else {
+          log?.show();
+          await vscode.window.showInformationMessage(
+            "Files without matches are listed in the Patchloom output channel."
+          );
+        }
+      }
+    },
     {
       label: "Create a new file",
       description: "Scaffold a new file in the workspace",
@@ -440,8 +489,8 @@ export async function runQuickAction(): Promise<void> {
         }
 
         const selector = await vscode.window.showInputBox({
-          prompt: "Selector path",
-          placeHolder: "scripts.test",
+          prompt: "Selector path (CLI 0.30+ accepts numeric compares such as servers[port>8000])",
+          placeHolder: "scripts.test or servers[port>8000]",
           validateInput: (value) => value.length > 0 ? undefined : "Selector is required."
         });
         if (selector === undefined) {
@@ -1097,16 +1146,26 @@ export function buildDocSetQuickAction(targetPath: string, selector: string, val
   };
 }
 
-export function buildSearchQuickAction(workspacePath: string, pattern: string, glob?: string): PlannedQuickAction {
+export function buildSearchQuickAction(
+  workspacePath: string,
+  pattern: string,
+  glob?: string,
+  options?: { readonly filesWithoutMatch?: boolean }
+): PlannedQuickAction {
   const args: string[] = ["search", pattern];
+  if (options?.filesWithoutMatch) {
+    args.push("--files-without-match");
+  }
   if (glob) {
     args.push("--glob", glob);
   }
   args.push(workspacePath);
   const targetIndex = args.length - 1;
 
   return {
-    title: `Search for "${pattern}"`,
+    title: options?.filesWithoutMatch
+      ? `Search files without "${pattern}"`
+      : `Search for "${pattern}"`,
     targetPath: workspacePath,
     targetArgIndices: [targetIndex],
     args

test/unit/binary.test.ts

@@ -276,8 +276,8 @@ test("preferredBinaryRemediationAction is undefined when ready and supported", (
     source: "path",
     message: "Using Patchloom from PATH.",
     binaryPath: "/usr/local/bin/patchloom",
-    version: "patchloom 0.28.0",
-    detectedVersion: "0.28.0",
+    version: "patchloom 0.31.0",
+    detectedVersion: "0.31.0",
     compatibility: "supported",
     minimumSupportedVersion: MINIMUM_SUPPORTED_PATCHLOOM_VERSION
   });

test/unit/initializeProject.test.ts

@@ -150,6 +150,32 @@ test("formatCliOutput surfaces empty path invalid_input (CLI 0.28+)", () => {
   );
 });
 
+test("formatCliOutput surfaces parent path invalid_input (CLI 0.31+)", () => {
+  const stdout = JSON.stringify({
+    ok: false,
+    error: "parent path is not a directory: /tmp/notdir",
+    error_kind: "invalid_input",
+    applied: false
+  });
+  assert.equal(
+    formatCliOutput({ exitCode: 1, stdout, stderr: "" }),
+    "invalid_input: parent path is not a directory: /tmp/notdir"
+  );
+});
+
+test("formatCliOutput surfaces numeric selector invalid_input (CLI 0.30+)", () => {
+  const stdout = JSON.stringify({
+    ok: false,
+    error: "selector error: comparison operand must be numeric (got 'abc' after >)",
+    error_kind: "invalid_input",
+    applied: false
+  });
+  assert.equal(
+    formatCliOutput({ exitCode: 1, stdout, stderr: "" }),
+    "invalid_input: selector error: comparison operand must be numeric (got 'abc' after >)"
+  );
+});
+
 test("formatCliOutput appends suggested_op when present (CLI 0.27+)", () => {
   const stdout = JSON.stringify({
     ok: false,

test/unit/patchloomCli.test.ts

@@ -29,6 +29,7 @@ import {
   buildApplyFragmentQuickAction,
   buildInsertAfterMatchQuickAction,
   buildReplaceQuickAction,
+  buildSearchQuickAction,
   retargetQuickAction,
   withApplyFlag
 } from "../../src/commands/quickActions.js";
@@ -581,6 +582,56 @@ describe("patchloom CLI integration", async () => {
     });
   });
 
+  test("search --files-without-match via Quick Action args (CLI 0.29+)", async (t) => {
+    const { stdout, stderr } = await execFileAsync(binaryPath, ["--version"], { timeout: 5000 });
+    const version = parsePatchloomVersion(`${stdout}${stderr}`);
+    if (!version || comparePatchloomVersions(version, "0.29.0") < 0) {
+      t.skip(`requires patchloom >= 0.29.0 (found ${version ?? "unknown"})`);
+      return;
+    }
+
+    await withTempDir(async (dir) => {
+      await fs.writeFile(path.join(dir, "hit.txt"), "TODO\n", "utf8");
+      await fs.writeFile(path.join(dir, "miss.txt"), "ok\n", "utf8");
+
+      const action = buildSearchQuickAction(dir, "TODO", undefined, { filesWithoutMatch: true });
+      const result = await execFileAsync(binaryPath, ["--json", ...action.args], { timeout: 5000 });
+      const parsed = JSON.parse(result.stdout) as {
+        files?: Array<{ path?: string }>;
+      };
+      const files = (parsed.files ?? []).map((entry) => path.basename(entry.path ?? ""));
+      assert.ok(files.includes("miss.txt"), "files without the pattern should be listed");
+      assert.ok(!files.includes("hit.txt"), "files that contain the pattern should be omitted");
+    });
+  });
+
+  test("create through a file parent is invalid_input (CLI 0.31+)", async (t) => {
+    const { stdout, stderr } = await execFileAsync(binaryPath, ["--version"], { timeout: 5000 });
+    const version = parsePatchloomVersion(`${stdout}${stderr}`);
+    if (!version || comparePatchloomVersions(version, "0.31.0") < 0) {
+      t.skip(`requires patchloom >= 0.31.0 (found ${version ?? "unknown"})`);
+      return;
+    }
+
+    await withTempDir(async (dir) => {
+      const parent = path.join(dir, "notdir");
+      await fs.writeFile(parent, "file\n", "utf8");
+      const dest = path.join(parent, "child.txt");
+
+      try {
+        await execFileAsync(binaryPath, ["--json", "create", dest, "--content", "x", "--apply"], {
+          timeout: 5000
+        });
+        assert.fail("create through a file parent should fail");
+      } catch (error) {
+        const failed = error as { stdout?: string; stderr?: string };
+        const payload = `${failed.stdout ?? ""}${failed.stderr ?? ""}`;
+        assert.match(payload, /parent path is not a directory/);
+        assert.match(payload, /invalid_input/);
+      }
+    });
+  });
+
   test("doc append adds an item to a JSON array", async () => {
     await withTempDir(async (dir) => {
       const file = path.join(dir, "config.json");

test/unit/quickActions.test.ts

@@ -266,6 +266,28 @@ test("buildSearchQuickAction includes glob when provided", () => {
   assert.deepEqual(action.targetArgIndices, [4]);
 });
 
+test("buildSearchQuickAction includes --files-without-match (CLI 0.29+)", () => {
+  const action = buildSearchQuickAction("/workspace/demo", "TODO", undefined, {
+    filesWithoutMatch: true
+  });
+
+  assert.equal(action.title, 'Search files without "TODO"');
+  assert.deepEqual(action.args, ["search", "TODO", "--files-without-match", "/workspace/demo"]);
+  assert.deepEqual(action.targetArgIndices, [3]);
+});
+
+test("buildSearchQuickAction combines --files-without-match with glob", () => {
+  const action = buildSearchQuickAction("/workspace/demo", "TODO", "*.ts", {
+    filesWithoutMatch: true
+  });
+
+  assert.equal(action.title, 'Search files without "TODO"');
+  assert.deepEqual(action.args, [
+    "search", "TODO", "--files-without-match", "--glob", "*.ts", "/workspace/demo"
+  ]);
+  assert.deepEqual(action.targetArgIndices, [5]);
+});
+
 test("buildCreateQuickAction builds a create command with content and apply", () => {
   const action = buildCreateQuickAction("/workspace/demo/src/newfile.ts", "hello");
 

walkthrough/initialize.md

@@ -6,7 +6,8 @@ your codebase.
 Click **Initialize Project** above to run `patchloom agent-rules` in
 your workspace. You can choose integration mode (CLI + MCP, CLI only, or
 MCP only), shell platform examples (all, Linux/macOS, or Windows), and
-surface (full document or core pack for system-prompt injection).
+surface (full document or core pack for system-prompt injection). On
+CLI 0.29+, the core pack text follows the mode you pick.
 
 ## What AGENTS.md Contains