Fix nonDottedPaths handling in cli flow lock generation

cli/src/commands/flow/flow_metadata.ts

@@ -29,7 +29,10 @@ import { FlowFile } from "./flow.ts";
 import { FlowValue } from "../../../gen/types.gen.ts";
 import { replaceInlineScripts } from "../../../windmill-utils-internal/src/inline-scripts/replacer.ts";
 import { workspaceDependenciesLanguages } from "../../utils/script_common.ts";
-import { extractNameFromFolder, getFolderSuffix } from "../../utils/resource_folders.ts";
+import {
+  extractNameFromFolder,
+  getNonDottedPaths,
+} from "../../utils/resource_folders.ts";
 
 const TOP_HASH = "__flow_hash";
 async function generateFlowHash(
@@ -157,7 +160,9 @@ export async function generateFlowLockInternal(
       filteredDeps
     );
 
-    const lockAssigner = newPathAssigner(opts.defaultTs ?? "bun");
+    const lockAssigner = newPathAssigner(opts.defaultTs ?? "bun", {
+      skipInlineScriptSuffix: getNonDottedPaths(),
+    });
     const inlineScripts = extractInlineScriptsForFlows(
       flowValue.value.modules,
       {},

cli/test/sync_pull_push.test.ts

@@ -1768,6 +1768,66 @@ excludes: []
     });
   });
 
+test("Integration: Sync pull with nonDottedPaths uses non-dotted inline script filenames", async () => {
+    await withTestBackend(async (backend, tempDir) => {
+      // Push a flow using default dotted paths
+      await writeFile(
+        `${tempDir}/wmill.yaml`,
+        `defaultTs: bun
+includes:
+  - "**"
+excludes: []
+`,
+      "utf-8",
+      );
+
+      const uniqueId = Date.now();
+      const flowName = `f/test/nondot_pull_inline_${uniqueId}`;
+      const flowFixture = createFlowFixture(flowName);
+      await mkdir(`${tempDir}/f/test/nondot_pull_inline_${uniqueId}${getFolderSuffix("flow")}`, { recursive: true });
+      for (const file of Object.values(flowFixture)) {
+        await writeFile(`${tempDir}/${file.path}`, file.content, "utf-8");
+      }
+
+      const pushResult = await backend.runCLICommand(
+        ["sync", "push", "--yes", "--includes", `f/test/nondot_pull_inline_${uniqueId}*/**`],
+        tempDir,
+      );
+      expect(pushResult.code).toEqual(0);
+
+      // Pull into a fresh directory with nonDottedPaths enabled
+      const tempDir2 = await mkdtemp(join(tmpdir(), "wmill_nondot_inline_"));
+      try {
+        await writeFile(
+          `${tempDir2}/wmill.yaml`,
+          `defaultTs: bun
+nonDottedPaths: true
+includes:
+  - "**"
+excludes: []
+`,
+        "utf-8",
+        );
+
+        const pullResult = await backend.runCLICommand(["sync", "pull", "--yes"], tempDir2);
+        expect(pullResult.code).toEqual(0);
+
+        // Verify pulled files use non-dotted inline script naming
+        const files = await listFilesRecursive(tempDir2);
+        const flowFiles = files.filter((f) => f.includes(`nondot_pull_inline_${uniqueId}`));
+
+        expect(flowFiles.length > 0).toBeTruthy();
+        // Should use __flow folder, not .flow
+        expect(flowFiles.some((f) => f.includes("__flow/"))).toBeTruthy();
+        // No files should have .inline_script. in their name
+        const dottedInlineFiles = flowFiles.filter((f) => f.includes(".inline_script."));
+        expect(dottedInlineFiles.length).toEqual(0);
+      } finally {
+        await cleanupTempDir(tempDir2);
+      }
+    });
+  });
+
 // =============================================================================
 // ws_error_handler_muted Persistence Tests
 // =============================================================================

cli/test/unified_generate_metadata.test.ts

@@ -8,7 +8,7 @@
 import { expect, test, describe } from "bun:test";
 import { withTestBackend } from "./test_backend.ts";
 import { addWorkspace } from "../workspace.ts";
-import { writeFile } from "node:fs/promises";
+import { mkdir, readFile, stat, writeFile } from "node:fs/promises";
 import {
   createLocalScript,
   createLocalFlow,
@@ -19,7 +19,12 @@ import {
 /**
  * Helper to set up a workspace with wmill.yaml
  */
-async function setupWorkspace(backend: any, tempDir: string, workspaceName: string) {
+async function setupWorkspace(
+  backend: any,
+  tempDir: string,
+  workspaceName: string,
+  nonDottedPaths = false
+) {
   const testWorkspace = {
     remote: backend.baseUrl,
     workspaceId: backend.workspace,
@@ -29,11 +34,88 @@ async function setupWorkspace(backend: any, tempDir: string, workspaceName: stri
   await addWorkspace(testWorkspace, { force: true, configDir: backend.testConfigDir });
 
   await writeFile(`${tempDir}/wmill.yaml`, `defaultTs: bun
-includes:
+${nonDottedPaths ? "nonDottedPaths: true\n" : ""}includes:
   - "**"
 excludes: []`, "utf-8");
 }
 
+async function createLocalNonDottedFlow(tempDir: string, name: string) {
+  const flowDir = `${tempDir}/f/test/${name}__flow`;
+  await mkdir(flowDir, { recursive: true });
+
+  await writeFile(
+    `${flowDir}/a.ts`,
+    `export async function main() {\n  return "Hello from flow ${name}";\n}`,
+    "utf-8"
+  );
+
+  await writeFile(
+    `${flowDir}/flow.yaml`,
+    `summary: "${name} flow"
+description: "A flow for testing"
+value:
+  modules:
+    - id: a
+      value:
+        type: rawscript
+        content: "!inline a.ts"
+        language: bun
+        input_transforms: {}
+schema:
+  $schema: "https://json-schema.org/draft/2020-12/schema"
+  type: object
+  properties: {}
+  required: []
+`,
+    "utf-8"
+  );
+}
+
+async function createLocalNonDottedApp(tempDir: string, name: string) {
+  const appDir = `${tempDir}/f/test/${name}__app`;
+  await mkdir(appDir, { recursive: true });
+
+  await writeFile(
+    `${appDir}/app.yaml`,
+    `summary: "${name} app"
+value:
+  type: app
+  grid:
+    - id: button1
+      data:
+        type: buttoncomponent
+        componentInput:
+          type: runnable
+          runnable:
+            type: runnableByName
+            inlineScript:
+              content: |
+                export async function main() {
+                  return "hello from app";
+                }
+              language: bun
+  hiddenInlineScripts: []
+  css: {}
+  norefreshbar: false
+policy:
+  on_behalf_of: null
+  on_behalf_of_email: null
+  triggerables: {}
+  execution_mode: viewer
+`,
+    "utf-8"
+  );
+}
+
+async function fileExists(filePath: string): Promise<boolean> {
+  try {
+    await stat(filePath);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
 // =============================================================================
 // Main test: processes scripts, flows, and apps together
 // =============================================================================
@@ -156,6 +238,87 @@ describe("generate-metadata flags", () => {
     });
   });
 
+  test("--lock-only preserves non-dotted flow filenames", async () => {
+    await withTestBackend(async (backend, tempDir) => {
+      await setupWorkspace(backend, tempDir, "lock_only_non_dotted_test", true);
+
+      await createLocalNonDottedFlow(tempDir, "my_flow");
+
+      const result = await backend.runCLICommand(
+        ["generate-metadata", "--yes", "--lock-only"],
+        tempDir,
+        "lock_only_non_dotted_test"
+      );
+
+      expect(result.code).toEqual(0);
+
+      const flowDir = `${tempDir}/f/test/my_flow__flow`;
+      const flowYaml = await readFile(`${flowDir}/flow.yaml`, "utf-8");
+
+      expect(flowYaml).toContain("!inline a.ts");
+      expect(flowYaml).toContain("!inline a.lock");
+      expect(flowYaml).not.toContain(".inline_script.");
+      expect(await fileExists(`${flowDir}/a.lock`)).toEqual(true);
+      expect(await fileExists(`${flowDir}/a.inline_script.ts`)).toEqual(false);
+      expect(await fileExists(`${flowDir}/a.inline_script.lock`)).toEqual(false);
+    });
+  });
+
+  test("generate-metadata preserves non-dotted flow inline script filenames", async () => {
+    await withTestBackend(async (backend, tempDir) => {
+      await setupWorkspace(backend, tempDir, "full_gen_non_dotted_flow_test", true);
+
+      await createLocalNonDottedFlow(tempDir, "my_flow");
+
+      const result = await backend.runCLICommand(
+        ["generate-metadata", "--yes"],
+        tempDir,
+        "full_gen_non_dotted_flow_test"
+      );
+
+      expect(result.code).toEqual(0);
+
+      const flowDir = `${tempDir}/f/test/my_flow__flow`;
+      const flowYaml = await readFile(`${flowDir}/flow.yaml`, "utf-8");
+
+      // Inline script references should use non-dotted naming
+      expect(flowYaml).toContain("!inline a.ts");
+      expect(flowYaml).toContain("!inline a.lock");
+      expect(flowYaml).not.toContain(".inline_script.");
+      expect(await fileExists(`${flowDir}/a.ts`)).toEqual(true);
+      expect(await fileExists(`${flowDir}/a.lock`)).toEqual(true);
+      expect(await fileExists(`${flowDir}/a.inline_script.ts`)).toEqual(false);
+      expect(await fileExists(`${flowDir}/a.inline_script.lock`)).toEqual(false);
+    });
+  });
+
+  test("generate-metadata uses non-dotted app inline script filenames", async () => {
+    await withTestBackend(async (backend, tempDir) => {
+      await setupWorkspace(backend, tempDir, "non_dotted_app_gen_test", true);
+
+      await createLocalNonDottedApp(tempDir, "my_app");
+
+      const result = await backend.runCLICommand(
+        ["generate-metadata", "--yes"],
+        tempDir,
+        "non_dotted_app_gen_test"
+      );
+
+      expect(result.code).toEqual(0);
+
+      const appDir = `${tempDir}/f/test/my_app__app`;
+      const appYaml = await readFile(`${appDir}/app.yaml`, "utf-8");
+
+      // Inline script references should use non-dotted naming
+      expect(appYaml).not.toContain(".inline_script.");
+      // Verify no dotted inline script files were created
+      const { readdir: readdirAsync } = await import("node:fs/promises");
+      const files = await readdirAsync(appDir);
+      const dottedFiles = files.filter((f: string) => f.includes(".inline_script."));
+      expect(dottedFiles.length).toEqual(0);
+    });
+  });
+
   test("--schema-only only processes scripts (skips flows and apps)", async () => {
     await withTestBackend(async (backend, tempDir) => {
       await setupWorkspace(backend, tempDir, "schema_only_test");