fix(workspace): unify nested project discovery and run ownership (#1716)

* fix(build): scope Kotlin bridge to linked Maven modules

* fix(run): resolve nested Go modules for context runs

* fix(gradle): discover nested builds and select compatible JVMs

* fix(workspace): share project discovery and module ownership

* fix(run): keep root toolchains for nested modules and resolve them once per module

- Python run configurations of a nested module without its own virtualenv use the closest one up to the project root.
- Gradle builds and runs fall back to the JDK matching the project's Java version when the Gradle version is unknown.
- Module-local interpreters and toolchains are resolved lazily, once per owning module.
- Tests build expected paths per segment so they hold on Windows.

src/features/run/configs.test.ts

@@ -235,6 +235,43 @@ describe("context configuration", () => {
     ]);
   });
 
+  it("does not borrow another Go module's run or test configuration", () => {
+    const go = [
+      cfg({ id: "go:run:api", kind: "go", command: "go", args: ["run", "."], cwd: "api" }),
+      cfg({ id: "go:test:api", kind: "go", command: "go", args: ["test", "./..."], cwd: "api", isTest: true }),
+    ];
+    expect(contextConfig("other/main.go", go, "package main\nfunc main() {}")).toBeNull();
+    expect(contextConfig("other/main_test.go", go, "package main")).toBeNull();
+  });
+
+  it("uses a nested Go module even when only the parent has a run configuration", () => {
+    const go = [
+      cfg({ id: "go:run", kind: "go", command: "go", args: ["run", "."] }),
+      cfg({ id: "go:test:api", kind: "go", command: "go", args: ["test", "./..."], cwd: "api", isTest: true }),
+    ];
+    expect(contextConfig("api/tool/main.go", go, "package main\nfunc main() {}")).toMatchObject({
+      cwd: "api",
+      args: ["run", "./tool"],
+    });
+  });
+
+  it("does not pass typed Go test flags to an application build", () => {
+    const go = cfg({
+      id: "user:go-test",
+      kind: "go",
+      command: "go",
+      args: ["test", "-count=1", "./..."],
+      isTest: true,
+      params: { goKind: "test", module: "api", toolArgs: "-count=1" },
+    });
+    expect(contextConfig("api/cmd/server/main.go", [go], "package main\nfunc main() {}")).toMatchObject({
+      cwd: "api",
+      args: ["run", "./cmd/server"],
+      params: undefined,
+      isTest: false,
+    });
+  });
+
   it("finds run targets and script invocations", () => {
     expect(contextConfig("src/bin/server.rs", configs)!.id).toBe("cargo:run:server");
     expect(contextConfig("tools/gen.py", configs)).toMatchObject({

src/features/run/context.ts

@@ -7,6 +7,7 @@ import type { RunConfig } from "@/platform/ipc";
 import { djangoLabel, djangoTestsOf, hasDjangoTests } from "./djangoTypes";
 import { phpunitArgs } from "./testing/phpunit";
 import { goTestParts } from "./goArguments";
+import { goBuildType } from "./goTypes";
 import { isWindows } from "./jvmTypes";
 
 export type FileRole = "test" | "main" | "script" | null;
@@ -51,16 +52,28 @@ function testKinds(relPath: string): string[] {
   return [];
 }
 
+/** The module owning a configuration's targets, relative to the project root. */
+export function configScope(config: RunConfig): string {
+  return (
+    config.kind === "go"
+      ? (config.params?.module ?? config.module ?? config.cwd ?? "")
+      : (config.module ?? config.cwd ?? "")
+  )
+    .replace(/^\.(?:\/|$)/, "")
+    .replace(/\/+$/, "");
+}
+
 /** Configs whose working directory most specifically contains `relPath` (ties in their original order). */
-function allClosest(configs: RunConfig[], relPath: string): RunConfig[] {
+export function allClosest(configs: readonly RunConfig[], relPath: string): RunConfig[] {
   const score = (c: RunConfig) => {
-    const cwd = (c.kind === "go" ? (c.params?.module ?? c.cwd ?? "") : (c.cwd ?? ""))
-      .replace(/^\.\/?/, "")
-      .replace(/\/+$/, "");
+    const cwd = configScope(c);
     if (!cwd) return 0;
     return relPath === cwd || relPath.startsWith(cwd + "/") ? cwd.length : -1;
   };
-  const scored = configs.map((c) => [c, score(c)] as const).filter(([, s]) => s >= 0);
+  const scored = configs
+    .filter((c) => !c.id.startsWith("context:"))
+    .map((c) => [c, score(c)] as const)
+    .filter(([, s]) => s >= 0);
   const best = Math.max(...scored.map(([, s]) => s));
   return scored.filter(([, s]) => s === best).map(([c]) => c);
 }
@@ -72,10 +85,10 @@ function closest(configs: RunConfig[], relPath: string): RunConfig | undefined {
 
 /** `relPath` relative to the working directory of `config`. */
 export function relToCwd(relPath: string, config: RunConfig): string {
-  const cwd = (config.kind === "go" ? (config.params?.module ?? config.cwd ?? "") : (config.cwd ?? ""))
-    .replace(/^\.\/?/, "")
+  const cwd = (config.kind === "go" ? configScope(config) : (config.cwd ?? ""))
+    .replace(/^\.(?:\/|$)/, "")
     .replace(/\/+$/, "");
-  return cwd && relPath.startsWith(cwd + "/") ? relPath.slice(cwd.length + 1) : relPath;
+  return relPath === cwd ? "" : cwd && relPath.startsWith(cwd + "/") ? relPath.slice(cwd.length + 1) : relPath;
 }
 
 function derived(base: RunConfig, relPath: string, patch: Partial<RunConfig>): RunConfig {
@@ -94,14 +107,22 @@ function derived(base: RunConfig, relPath: string, patch: Partial<RunConfig>): R
  * The project's Python interpreter as `(command, leading args)`, derived from
  * detected configs (venv / uv / poetry), or null when none says.
  */
-export function projectPython(configs: RunConfig[]): { command: string; prefix: string[] } | null {
+export function projectPython(configs: RunConfig[], relPath?: string): { command: string; prefix: string[] } | null {
+  if (relPath !== undefined)
+    configs = allClosest(
+      configs.filter((c) => ["python", "pytest", "django-test"].includes(c.kind)),
+      relPath,
+    );
   const py = configs.find((c) => c.kind === "python");
   if (py) {
     // The interpreter part ends where the program starts: `-m`, or the script (`manage.py`). What follows
     // (`runserver`, `test`…) belongs to that program, never to the interpreter.
     const end = py.args.findIndex((a) => a === "-m" || a.endsWith(".py"));
     const python = py.args.findIndex((a) => /^python[\d.]*$/.test(a));
-    return { command: py.command, prefix: py.args.slice(0, end >= 0 ? end : python + 1) };
+    return {
+      command: py.command,
+      prefix: py.args.slice(0, end >= 0 ? end : python + 1),
+    };
   }
   const pytest = configs.find((c) => c.kind === "pytest");
   if (!pytest) return null;
@@ -120,15 +141,20 @@ export function projectPython(configs: RunConfig[]): { command: string; prefix:
  */
 function implicitPytest(relPath: string, configs: RunConfig[]): RunConfig | null {
   if (!relPath.endsWith(".py")) return null;
-  const py = projectPython(configs);
+  const owners = allClosest(
+    configs.filter((c) => ["python", "pytest", "django-test"].includes(c.kind)),
+    relPath,
+  );
+  const py = projectPython(owners);
   return {
     id: "pytest:implicit",
     name: "pytest",
     kind: "pytest",
     command: py?.command ?? "python3",
     args: [...(py?.prefix ?? []), "-m", "pytest"],
-    cwd: null,
-    env: {},
+    cwd: owners[0]?.cwd ?? null,
+    module: owners[0]?.module,
+    env: { ...owners[0]?.env },
     detected: true,
     isTest: true,
     debugAdapter: "debugpy",
@@ -147,7 +173,7 @@ export function testBasesFor(relPath: string, configs: RunConfig[]): RunConfig[]
     .sort((a, b) => kinds.indexOf(a.kind) - kinds.indexOf(b.kind));
   const best = allClosest(candidates, relPath);
   if (best.length) return best;
-  const fallback = candidates[0] ?? implicitPytest(relPath, configs);
+  const fallback = implicitPytest(relPath, configs);
   return fallback ? [fallback] : [];
 }
 
@@ -213,21 +239,47 @@ export function testConfigFor(relPath: string, configs: RunConfig[], base?: RunC
 function mainConfigFor(relPath: string, configs: RunConfig[]): RunConfig | null {
   if (relPath.endsWith(".rs")) {
     const bin = /src\/bin\/([^/]+)\.rs$/.exec(relPath)?.[1];
-    const runs = configs.filter((c) => c.kind === "cargo" && c.id.startsWith("cargo:run"));
+    const runs = allClosest(
+      configs.filter((c) => c.kind === "cargo" && c.args[0] === "run"),
+      relPath,
+    );
     const byBin = bin ? runs.find((c) => c.id === `cargo:run:${bin}` || c.args.includes(bin)) : undefined;
-    return byBin ?? closest(runs, relPath) ?? runs[0] ?? null;
+    return byBin ?? runs[0] ?? null;
   }
   if (relPath.endsWith(".go")) {
-    const gos = configs.filter((c) => c.kind === "go");
-    const runs = gos.filter((c) => c.args[0] === "run");
+    const gos = allClosest(
+      configs.filter((c) => c.kind === "go" && !c.id.startsWith("context:")),
+      relPath,
+    );
+    const runs = gos.filter((c) => c.args[0] === "run" || c.params?.goKind === "build");
     // The module containing the file (nested modules run from their own directory).
-    const base = closest(runs, relPath) ?? closest(gos, relPath) ?? runs[0] ?? gos[0];
+    const base = runs[0] ?? gos[0];
     if (!base) return null;
     const dir = dirOf(relToCwd(relPath, base));
     const target = dir ? `./${dir}` : ".";
-    const hit = runs.find((c) => (c.cwd ?? "") === (base.cwd ?? "") && c.args[1] === target);
+    if (base.params?.goKind === "build") {
+      const params = {
+        ...base.params,
+        goKind: "build",
+        scope: "package",
+        target,
+        runAfterBuild: "true",
+      };
+      return derived(base, relPath, {
+        ...goBuildType.commandLine(params),
+        params,
+        name: `go run ${target}`,
+        isTest: false,
+      });
+    }
+    const hit = runs.find((c) => configScope(c) === configScope(base) && c.args[1] === target);
     if (hit) return hit;
-    return derived(base, relPath, { args: ["run", target], name: `go run ${target}`, isTest: false });
+    return derived(base, relPath, {
+      args: ["run", target],
+      name: `go run ${target}`,
+      isTest: false,
+      ...(base.params?.goKind === "test" ? { params: undefined, cwd: base.params.module ?? base.cwd } : {}),
+    });
   }
   if (/\.(kt|java)$/.test(relPath)) {
     // The build containing the file (builds nested in a folder of repositories carry a `:<dir>` suffix).

src/features/run/producers.test.ts

@@ -1,4 +1,5 @@
-import { afterEach, describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import * as projectRoots from "@/platform/projectRoots";
 import type { HierarchyItem, RunConfig } from "@/platform/ipc";
 import {
   innermostTarget,
@@ -273,6 +274,82 @@ describe("single-file producers (scratches)", () => {
     expect(p.config).toMatchObject({ args: ["run", "./cmd/tool"] });
   });
 
+  it("Go: nested modules win over previous single-file runs", () => {
+    const go = [
+      cfg({
+        id: "context:file:fixtures/go-app/cmd/server/main.go",
+        kind: "go",
+        args: ["run", "fixtures/go-app/cmd/server/main.go"],
+      }),
+      cfg({
+        id: "go:run:server:fixtures/go-app",
+        kind: "go",
+        args: ["run", "./cmd/server"],
+        cwd: "fixtures/go-app",
+      }),
+    ];
+    const input = {
+      path: `${ROOT}/fixtures/go-app/cmd/server/main.go`,
+      root: ROOT,
+      configs: go,
+      content: "package main\nfunc main() {}",
+    };
+    for (const line of [undefined, 1]) {
+      expect(produceContext({ ...input, line }, ALL)?.config).toMatchObject({
+        id: "go:run:server:fixtures/go-app",
+        args: ["run", "./cmd/server"],
+        cwd: "fixtures/go-app",
+      });
+    }
+  });
+
+  it("Go: single-file runs never become module configurations", () => {
+    const input = {
+      path: `${ROOT}/standalone/main.go`,
+      root: ROOT,
+      configs: [] as RunConfig[],
+      content: "package main\nfunc main() {}",
+    };
+    const first = produceContext(input, ALL)!;
+    expect(first.config).toMatchObject({ id: "context:file:standalone/main.go", args: ["run", "standalone/main.go"] });
+    expect(produceContext({ ...input, configs: [first.config!] }, ALL)?.config).toEqual(first.config);
+  });
+
+  it("Go: typed modules own only their own files", () => {
+    const configs = [
+      ...["api", "worker"].map((module) =>
+        cfg({
+          id: `go:run:${module}`,
+          kind: "go",
+          args: ["build", "-race", "."],
+          params: { module, goKind: "build", scope: "package", target: ".", toolArgs: "-race" },
+        }),
+      ),
+    ];
+    for (const module of ["api", "worker"]) {
+      expect(
+        produceContext(
+          {
+            path: `${ROOT}/${module}/cmd/server/main.go`,
+            root: ROOT,
+            configs,
+            content: "package main\nfunc main() {}",
+          },
+          ALL,
+        )?.config,
+      ).toMatchObject({
+        args: ["build", "-race", "./cmd/server"],
+        params: { module, target: "./cmd/server", goKind: "build", runAfterBuild: "true" },
+      });
+    }
+    expect(
+      produceContext(
+        { path: `${ROOT}/standalone/main.go`, root: ROOT, configs, content: "package main\nfunc main() {}" },
+        ALL,
+      )?.config,
+    ).toMatchObject({ id: "context:file:standalone/main.go", args: ["run", "standalone/main.go"] });
+  });
+
   it("Rust: rustc into the compile directory, then the binary; codelldb debugs the binary", () => {
     const p = produceContext(scratch("hihi.rs", 'fn main() {\n  println!("hi");\n}'), ALL)!;
     expect(p.name).toBe("hihi.rs");
@@ -1003,3 +1080,109 @@ describe("CMake file context", () => {
     expect(p?.missing?.body).toContain("CMake Configure");
   });
 });
+
+describe("module ownership across languages", () => {
+  it.each([
+    ["npm", "other.test.ts", ["run", "test"]],
+    ["deno", "other.test.ts", ["test"]],
+    ["cargo", "tests/other.rs", ["test"]],
+    ["go", "other_test.go", ["test", "./..."]],
+    ["phpunit", "OtherTest.php", []],
+    ["rspec", "other_spec.rb", []],
+    ["maven", "OtherTest.java", ["test"]],
+    ["gradle", "OtherTest.kt", ["test"]],
+  ])("%s never borrows a sibling test configuration", (kind, file, args) => {
+    const configs = [cfg({ id: "sibling", kind, args, cwd: "apps/one", isTest: true })];
+    const result = produceFile({ root: ROOT, path: `${ROOT}/apps/two/${file}`, configs }, OPTIMISTIC);
+    expect(result?.config?.id ?? "").not.toContain("sibling");
+  });
+
+  it("selects the nearest Python interpreter and ignores temporary configs", () => {
+    const configs = [
+      cfg({
+        id: "one",
+        kind: "pytest",
+        command: "/env/one/bin/pytest",
+        cwd: "one",
+        isTest: true,
+      }),
+      cfg({
+        id: "two",
+        kind: "pytest",
+        command: "/env/two/bin/pytest",
+        cwd: "two",
+        isTest: true,
+      }),
+      cfg({
+        id: "context:old",
+        kind: "python",
+        command: "/env/stale/python",
+        cwd: "two",
+      }),
+    ];
+    expect(produceFile({ root: ROOT, path: `${ROOT}/two/main.py`, configs }, OPTIMISTIC)?.config?.command).toBe(
+      "/env/two/bin/python",
+    );
+  });
+
+  it("a Cargo package owns its binary even when commands run at the workspace root", () => {
+    const configs = [
+      cfg({
+        id: "cargo:run:one",
+        kind: "cargo",
+        module: "crates/one",
+        args: ["run", "-p", "one", "--bin", "server"],
+      }),
+      cfg({
+        id: "workspace:member:cargo:run:two",
+        kind: "cargo",
+        module: "crates/two",
+        args: ["run", "-p", "two", "--bin", "server"],
+      }),
+    ];
+    const result = produceFile({ root: ROOT, path: `${ROOT}/crates/two/src/bin/server.rs`, configs }, OPTIMISTIC);
+    expect(result?.config?.args).toEqual(configs[1]!.args);
+    expect(result?.config?.cwd).toBeNull();
+  });
+
+  it.each(["/work/app", "C:/work/app"])("matches absolute workspace configs under %s", (root) => {
+    const configs = [
+      cfg({
+        id: "test",
+        kind: "npm",
+        cwd: `${root}/apps/web`,
+        module: `${root}/apps/web`,
+        args: ["run", "test"],
+        isTest: true,
+      }),
+    ];
+    const result = produceFile({ root, path: `${root}/apps/web/a.test.ts`, configs }, OPTIMISTIC);
+    expect(result?.config).toMatchObject({
+      cwd: "apps/web",
+      args: ["run", "test", "--", "a.test.ts"],
+    });
+  });
+});
+
+it("runs scripts from their owning module with arguments relative to that directory", () => {
+  const configs = [cfg({ id: "web", kind: "npm", cwd: "apps/web", module: "apps/web" })];
+  expect(produceFile({ root: ROOT, path: `${ROOT}/apps/web/src/main.js`, configs }, OPTIMISTIC)?.config).toMatchObject({
+    cwd: "apps/web",
+    args: ["src/main.js"],
+  });
+});
+
+it("nested Ruby scripts use their own source paths relative to their cwd", () => {
+  const spy = vi.spyOn(projectRoots, "currentRoots").mockReturnValue([
+    { path: "apps/ruby/lib", kind: "source", detectedFrom: null },
+    { path: "apps/other/lib", kind: "source", detectedFrom: null },
+  ]);
+  try {
+    const configs = [cfg({ id: "ruby", kind: "rake", cwd: "apps/ruby", args: ["test"] })];
+    expect(
+      produceFile({ root: ROOT, path: `${ROOT}/apps/ruby/bin/main.rb`, configs }, OPTIMISTIC)?.config,
+    ).toMatchObject({ cwd: "apps/ruby", args: ["-Ilib", "bin/main.rb"] });
+  } finally {
+    spy.mockRestore();
+  }
+});

src/features/run/producers.ts

@@ -10,13 +10,22 @@
  * globally installed tools.
  */
 import type { RunConfig } from "@/platform/ipc";
+import { ipcPath, isSameOrInside } from "@/platform/paths";
 import { isTestPath } from "@/platform/languageSettings";
 import { currentRoots } from "@/platform/projectRoots";
 import { applicationConfig, jvmModuleDir } from "./application";
 import { formatArgs } from "./configs";
 import { goGenerateConfig } from "./goGenerate";
 import { goTestParts } from "./goArguments";
-import { contextConfig, fileRole, projectPython, testBasesFor, testConfigFor } from "./context";
+import {
+  allClosest,
+  contextConfig,
+  fileRole,
+  projectPython,
+  testBasesFor,
+  testConfigFor,
+  relToCwd as relativeToCwd,
+} from "./context";
 import { djangoLabel, djangoTestsOf, hasDjangoTests } from "./djangoTypes";
 import { firstTopLevelType, scanJvmTargets, simpleClassName } from "./jvmTargets";
 import { isWindows } from "./jvmTypes";
@@ -103,6 +112,26 @@ function relTo(path: string, root: string | null): string {
   return root && path.startsWith(root + "/") ? path.slice(root.length + 1) : path;
 }
 
+function scopedInput<T extends Pick<ContextInput, "root" | "configs">>(input: T): T {
+  const root = input.root && ipcPath(input.root).replace(/\/+$/, "");
+  if (!root) return input;
+  const relative = (value: string) => {
+    const path = ipcPath(value);
+    return path === root ? "" : path.startsWith(root + "/") ? path.slice(root.length + 1) : path;
+  };
+  return {
+    ...input,
+    configs: input.configs.map((c) => ({
+      ...c,
+      cwd: c.cwd == null ? c.cwd : relative(c.cwd),
+      ...(c.module == null ? {} : { module: relative(c.module) }),
+      ...(c.kind === "go" && c.params?.module != null
+        ? { params: { ...c.params, module: relative(c.params.module) } }
+        : {}),
+    })),
+  };
+}
+
 /** Short stable hash, so compiled binaries of same-named files don't collide. */
 function hash(s: string): string {
   let h = 5381;
@@ -136,7 +165,7 @@ function mkdirLine(dir: string, windows = false): string {
 /** Absolute directory of a configuration's working directory (a Go module). */
 export function goModuleDir(root: string, cwd: string | null): string {
   const rel = (cwd ?? "").replace(/^\.(?:\/|$)/, "").replace(/\/+$/, "");
-  if (rel.startsWith("/")) return rel;
+  if (rel.startsWith("/") || /^[A-Za-z]:\//.test(rel)) return rel;
   return rel ? `${root}/${rel}` : root;
 }
 
@@ -384,10 +413,25 @@ function isProjectPath(input: Pick<ContextInput, "path" | "root" | "contentRoots
 function site(input: ContextInput): FileSite {
   const inside = isProjectPath(input);
   const rel = relTo(input.path, input.root);
+  const language = scriptLanguage(input.path, input.content);
+  const kinds: Record<string, string[]> = {
+    js: ["npm", "deno", "bun", "node"],
+    ts: ["npm", "deno", "bun", "node"],
+    python: ["python", "pytest", "django-test"],
+    ruby: ["ruby", "rake", "rspec"],
+    php: ["php", "phpunit", "composer"],
+  };
+  const owner =
+    inside && language
+      ? allClosest(
+          input.configs.filter((c) => kinds[language]?.includes(c.kind)),
+          rel,
+        )[0]
+      : undefined;
   return {
     idPath: rel,
-    arg: inside ? rel : baseName(input.path),
-    cwd: inside ? null : dirName(input.path),
+    arg: inside ? (owner ? relativeToCwd(rel, owner) : rel) : baseName(input.path),
+    cwd: inside ? owner?.cwd || null : dirName(input.path),
     file: baseName(input.path),
     inProject: inside,
   };
@@ -442,13 +486,21 @@ function pythonModule(input: ContextInput): { name: string; dir: string } | null
 /** Python: the interpreter from settings, the detected project interpreter, then `python3` on the PATH. */
 function pythonCommand(input: ContextInput, env: ToolEnv, s: FileSite): { command: string; prefix: string[] } | null {
   if (env.python) return { command: env.python, prefix: [] };
-  const py = projectPython([...input.configs]);
+  const py = projectPython([...input.configs], relTo(input.path, input.root));
   if (py) {
     // A venv-relative interpreter is relative to the project root.
+    const owner = allClosest(
+      input.configs.filter((c) => ["python", "pytest", "django-test"].includes(c.kind)),
+      relTo(input.path, input.root),
+    )[0];
+    const cwd = owner?.cwd ?? "";
+    const relativeCommand = py.command.includes("/") && !py.command.startsWith("/") && !/^[A-Za-z]:/.test(py.command);
     const command =
-      !s.inProject && input.root && py.command.includes("/") && !py.command.startsWith("/")
-        ? `${input.root}/${py.command.replace(/^\.\//, "")}`
-        : py.command;
+      relativeCommand && cwd
+        ? `${goModuleDir(input.root ?? "", cwd)}/${py.command.replace(/^\.\//, "")}`
+        : !s.inProject && input.root && relativeCommand
+          ? `${input.root}/${py.command.replace(/^\.\//, "")}`
+          : py.command;
     return { command, prefix: py.prefix };
   }
   const t = pick(env, ["python3", "python"]);
@@ -599,8 +651,20 @@ function simple(
 }
 
 /** `-I<dir>` for each Sources root of the project (the project root itself is already the cwd). */
-const rubyLoadPath = (roots: readonly { path: string; kind: string }[]): string[] =>
-  roots.filter((r) => r.kind === "source" && r.path !== "").map((r) => `-I${r.path}`);
+const rubyLoadPath = (
+  roots: readonly { path: string; kind: string }[],
+  cwd: string | null,
+  root: string | null,
+): string[] =>
+  roots
+    .filter((r) => r.kind === "source" && r.path !== "")
+    .flatMap((r) => {
+      if (!cwd) return [`-I${r.path}`];
+      const dir = goModuleDir(root ?? "", cwd);
+      const source = goModuleDir(root ?? "", r.path);
+      if (!isSameOrInside(source, dir)) return [];
+      return [`-I${source === dir ? "." : source.slice(dir.length + 1)}`];
+    });
 
 const hasGoMain = (content?: string) => content === undefined || /^\s*package\s+main\b/m.test(content);
 const hasRustMain = (content?: string) =>
@@ -614,11 +678,10 @@ const hasKotlinMain = (content?: string) => content === undefined || /^(?:suspen
  * directory at or above it): a build nested in a folder of repositories owns only its files.
  */
 function buildOwners(rel: string, configs: readonly RunConfig[], kinds: readonly string[]): RunConfig[] {
-  return configs.filter((c) => {
-    if (!kinds.includes(c.kind)) return false;
-    const cwd = (c.cwd ?? "").replace(/^\.\/?/, "").replace(/\/+$/, "");
-    return !cwd || rel.startsWith(cwd + "/");
-  });
+  return allClosest(
+    configs.filter((c) => kinds.includes(c.kind)),
+    rel,
+  );
 }
 
 const cargoOwner = (rel: string, configs: readonly RunConfig[]) => buildOwners(rel, configs, ["cargo"]);
@@ -655,6 +718,7 @@ function godotScene(rel: string, configs: readonly RunConfig[]): Produced | null
 
 /** The file as a whole: tests of a test file, the project's run target, or the runtime for its language. */
 export function produceFile(input: ContextInput, env: ToolEnv): Produced | null {
+  input = scopedInput(input);
   const s = site(input);
   const lang = scriptLanguage(input.path, input.content);
   const configs = [...input.configs];
@@ -685,12 +749,23 @@ export function produceFile(input: ContextInput, env: ToolEnv): Produced | null
     if (lang === "rust" && cargoOwner(rel, configs).length) {
       const example = /(?:^|\/)examples\/([^/]+)\.rs$/.exec(rel)?.[1];
       if (example && hasRustMain(input.content)) {
-        const base = cargoOwner(rel, configs).find((c) => c.id.startsWith("cargo:run")) ?? cargoOwner(rel, configs)[0]!;
+        const base = cargoOwner(rel, configs).find((c) => c.args[0] === "run") ?? cargoOwner(rel, configs)[0]!;
         const config: RunConfig = {
           ...base,
           id: `context:file:${rel}`,
           name: `Run ${example}`,
-          args: ["run", "--example", example],
+          args: [
+            "run",
+            ...base.args.flatMap((arg, i, args) =>
+              ["-p", "--package", "--manifest-path"].includes(arg)
+                ? [arg, args[i + 1]!]
+                : /^(?:--package=|--manifest-path=|-p.)/.test(arg)
+                  ? [arg]
+                  : [],
+            ),
+            "--example",
+            example,
+          ],
           env: { ...base.env },
           isTest: false,
           detected: true,
@@ -811,7 +886,10 @@ export function produceFile(input: ContextInput, env: ToolEnv): Produced | null
     }
     case "ruby":
       // Sources roots go on the load path (`-Ilib`), as `rake test` does; paths are project-relative.
-      return simple(lang, s, env, lang, () => [...(s.inProject ? rubyLoadPath(currentRoots()) : []), s.arg]);
+      return simple(lang, s, env, lang, () => [
+        ...(s.inProject ? rubyLoadPath(currentRoots(), s.cwd, input.root) : []),
+        s.arg,
+      ]);
     case "php":
       if (env.php) return { name: s.file, scope: "file", config: fileConfig(s, "php", env.php, [s.arg], "php-debug") };
       return simple(lang, s, env, lang, () => [s.arg], "php-debug");
@@ -926,6 +1004,7 @@ export function fileTargets(
   input: Pick<ContextInput, "path" | "root" | "configs" | "contentRoots">,
   content: string,
 ): RunTarget[] {
+  input = scopedInput(input);
   const s = { inProject: isProjectPath(input), rel: relTo(input.path, input.root) };
   const rust = /\.rs$/.test(input.path);
   if (/\.(c|cpp|cc|cxx)$/.test(input.path)) return standaloneTargets(content, input.path);
@@ -980,6 +1059,7 @@ function elementProduction(input: ContextInput, env: ToolEnv, target: RunTarget)
  * main function — else the file.
  */
 export function produceContext(input: ContextInput, env: ToolEnv): Produced | null {
+  input = scopedInput(input);
   if (input.content !== undefined && input.line !== undefined) {
     const targets = fileTargets(input, input.content.slice(0, 400_000));
     const inner = innermostTarget(input.content, targets, input.line, /\.(py|rb)$/.test(input.path));
@@ -997,6 +1077,7 @@ export function produceContext(input: ContextInput, env: ToolEnv): Produced | nu
  * like IDEA, the user then chooses one. A single production otherwise.
  */
 export function produceContextChoices(input: ContextInput, env: ToolEnv): Produced[] {
+  input = scopedInput(input);
   const produced = produceContext(input, env);
   if (!produced?.config || produced.scope === "directory" || !isProjectPath(input)) return produced ? [produced] : [];
   const rel = relTo(input.path, input.root);
@@ -1046,6 +1127,7 @@ function rubyDirectory(
   relToCwd: (c: RunConfig) => string,
   make: (base: RunConfig, label: string, args: string[]) => Produced,
   label: string,
+  root: string | null,
 ): Produced | null {
   const rspec = closest(["rspec"]);
   if (rspec) return make(rspec, label, [...rspec.args, relToCwd(rspec)]);
@@ -1058,13 +1140,14 @@ function rubyDirectory(
   const minitest = closest(["ruby"]);
   if (!minitest) return null;
   const at = minitest.args.indexOf("-e");
-  const flags = rubyLoadPath(currentRoots()).filter((f) => !minitest.args.includes(f));
+  const flags = rubyLoadPath(currentRoots(), minitest.cwd, root).filter((f) => !minitest.args.includes(f));
   const args = [...minitest.args.slice(0, -1)];
   args.splice(at < 0 ? args.length : at, 0, ...flags);
   return make(minitest, label, [...args, relToCwd(minitest)]);
 }
 
 export function produceDirectory(input: ContextInput): Produced | null {
+  input = scopedInput(input);
   const { root } = input;
   if (!root || !isProjectPath(input) || input.path === root) return null;
   const rel = relTo(input.path, root);
@@ -1074,26 +1157,23 @@ export function produceDirectory(input: ContextInput): Produced | null {
   const marked = isTestPath(currentRoots(), rel);
   const tests = input.configs.filter((c) => c.isTest);
   if (!TEST_DIR.test(rel) && !jvmRoot && !jvmPackage && !marked && !/(^|\/)src\/test(\/|$)/.test(rel)) return null;
-  const closest = (kinds: string[]) => {
-    const cands = tests.filter((c) => kinds.includes(c.kind));
-    const score = (c: RunConfig) => {
-      const cwd = (c.cwd ?? "").replace(/^\.\/?/, "").replace(/\/+$/, "");
-      if (!cwd) return 0;
-      return rel === cwd || rel.startsWith(cwd + "/") ? cwd.length : -1;
-    };
-    return cands
-      .map((c) => [c, score(c)] as const)
-      .filter(([, n]) => n >= 0)
-      .sort((a, b) => b[1] - a[1])[0]?.[0];
-  };
-  const relToCwd = (c: RunConfig) => {
-    const cwd = (c.cwd ?? "").replace(/^\.\/?/, "").replace(/\/+$/, "");
-    return cwd && rel.startsWith(cwd + "/") ? rel.slice(cwd.length + 1) : rel === cwd ? "" : rel;
-  };
+  const closest = (kinds: string[]) =>
+    allClosest(
+      tests.filter((c) => kinds.includes(c.kind)),
+      rel,
+    )[0];
+  const relToCwd = (c: RunConfig) => relativeToCwd(rel, c);
   const make = (base: RunConfig, label: string, args: string[]): Produced => ({
     name: label,
     scope: "directory",
-    config: { ...base, id: `context:dir:${base.id}:${rel}`, name: label, args, env: { ...base.env }, detected: true },
+    config: {
+      ...base,
+      id: `context:dir:${base.id}:${rel}`,
+      name: label,
+      args,
+      env: { ...base.env },
+      detected: true,
+    },
   });
   const testsIn = `Tests in '${name}'`;
 
@@ -1114,7 +1194,7 @@ export function produceDirectory(input: ContextInput): Produced | null {
     }
   }
   const js = closest(["npm", "bun", "deno"]);
-  const ruby = marked && !js && rubyDirectory(closest, relToCwd, make, testsIn);
+  const ruby = marked && !js && rubyDirectory(closest, relToCwd, make, testsIn, root);
   if (ruby) return ruby;
   const py = closest(["pytest"]);
   const django = closest(["django-test"]);

src/features/run/runtimes.test.ts

@@ -0,0 +1,43 @@
+import { beforeEach, expect, it, vi } from "vitest";
+
+const { entries, pythonNear } = vi.hoisted(() => ({
+  entries: new Map<string, string[]>(),
+  pythonNear: vi.fn(),
+}));
+vi.mock("@/platform/ipc", () => ({
+  isTauri: () => true,
+  call: (promise: Promise<unknown>) => promise,
+  commands: {
+    fsReadDir: async (dir: string) => (entries.get(dir) ?? []).map((name) => ({ name })),
+    sdkPythonEffective: pythonNear,
+    sdkLocateTools: async () => ({ compileDir: "/tmp/run", tools: [] }),
+  },
+}));
+import { clearRuntimeCache, rootMarkers, toolEnv } from "./runtimes";
+
+beforeEach(() => {
+  entries.clear();
+  pythonNear.mockReset().mockResolvedValue("/env/python");
+  clearRuntimeCache();
+});
+
+it("a nested runtime wins and a package boundary blocks a parent's runtime", async () => {
+  entries.set("/repo", ["deno.json"]);
+  entries.set("/repo/apps/node", ["package.json"]);
+  entries.set("/repo/apps/bun", ["bun.lock", "package.json"]);
+  expect(await rootMarkers("/repo", "/repo/apps/node/src/main.ts")).toEqual({ deno: false, bun: false });
+  expect(await rootMarkers("/repo", "/repo/apps/bun/src/main.ts")).toEqual({ deno: false, bun: true });
+  expect(await rootMarkers("/repo", "/repo/apps/deno/src/main.ts")).toEqual({ deno: true, bun: false });
+});
+
+it("a nested Deno project is discovered under a Node root", async () => {
+  entries.set("/repo", ["package.json"]);
+  entries.set("/repo/apps/deno", ["deno.jsonc"]);
+  expect(await rootMarkers("/repo", "/repo/apps/deno/main.ts")).toEqual({ deno: true, bun: false });
+});
+
+it("the production Python runtime query includes the source directory", async () => {
+  const env = await toolEnv(["python3"], "/repo/apps/python/src/main.py", "/repo", true);
+  expect(pythonNear).toHaveBeenCalledWith("/repo/apps/python/src");
+  expect(env.python).toBe("/env/python");
+});

src/features/run/runtimes.ts

@@ -78,9 +78,9 @@ export async function locateTools(
   return out;
 }
 
-async function projectPython(): Promise<string | null> {
+async function projectPython(file: string | null): Promise<string | null> {
   try {
-    return await call(commands.sdkPythonEffective());
+    return await call(commands.sdkPythonEffective(file ? dirOf(file) : null));
   } catch {
     return null;
   }
@@ -94,18 +94,23 @@ async function projectPhp(): Promise<string | null> {
   }
 }
 
-async function rootMarkers(root: string | null): Promise<{ deno: boolean; bun: boolean }> {
+export async function rootMarkers(root: string | null, file: string | null): Promise<{ deno: boolean; bun: boolean }> {
   if (!root) return { deno: false, bun: false };
-  try {
-    const entries = await call(commands.fsReadDir(root));
-    const names = new Set(entries.map((e) => e.name));
-    return {
-      deno: names.has("deno.json") || names.has("deno.jsonc"),
-      bun: names.has("bun.lockb") || names.has("bun.lock"),
-    };
-  } catch {
-    return { deno: false, bun: false };
+  let dir = file && file.startsWith(root + "/") ? dirOf(file) : root;
+  while (dir === root || dir.startsWith(root + "/")) {
+    try {
+      const entries = await call(commands.fsReadDir(dir));
+      const names = new Set(entries.map((e) => e.name));
+      const deno = names.has("deno.json") || names.has("deno.jsonc");
+      const bun = names.has("bun.lockb") || names.has("bun.lock");
+      if (deno || bun || names.has("package.json")) return { deno, bun };
+    } catch {
+      /* Unreadable ancestors contribute no runtime markers. */
+    }
+    if (dir === root) break;
+    dir = dirOf(dir);
   }
+  return { deno: false, bun: false };
 }
 
 /** The tool environment for running `file` with any of `names`. */
@@ -118,9 +123,11 @@ export async function toolEnv(
 ): Promise<ToolEnv> {
   const [tools, py, phpInterpreter, markers] = await Promise.all([
     locateTools(names, file),
-    python ? projectPython() : Promise.resolve(null),
+    python ? projectPython(file) : Promise.resolve(null),
     php ? projectPhp() : Promise.resolve(null),
-    names.includes("deno") || names.includes("bun") ? rootMarkers(root) : Promise.resolve({ deno: false, bun: false }),
+    names.includes("deno") || names.includes("bun")
+      ? rootMarkers(root, file)
+      : Promise.resolve({ deno: false, bun: false }),
   ]);
   return {
     tool: (n) => tools.get(n),