fix(bundler): use root option for filename comments in output

The filename comments in bundler output (e.g., `// src/entry.js`) were
computed relative to cwd instead of the configured `root` option. This
caused inconsistent output when running builds from different directories.

Changed `pathWithPrettyInitialized` and related path computations to
use `root_dir` when set, falling back to `top_level_dir` (cwd).

Fixes #3039

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/bundler/LinkerContext.zig

@@ -53,7 +53,8 @@ pub const LinkerContext = struct {
     }
 
     pub fn pathWithPrettyInitialized(this: *LinkerContext, path: Fs.Path) !Fs.Path {
-        return bundler.genericPathWithPrettyInitialized(path, this.options.target, this.resolver.fs.top_level_dir, this.allocator());
+        const root_dir = if (this.options.root_dir.len > 0) this.options.root_dir else this.resolver.fs.top_level_dir;
+        return bundler.genericPathWithPrettyInitialized(path, this.options.target, root_dir, this.allocator());
     }
 
     pub const LinkerOptions = struct {
@@ -75,6 +76,7 @@ pub const LinkerContext = struct {
         mode: Mode = .bundle,
 
         public_path: []const u8 = "",
+        root_dir: []const u8 = "",
 
         pub const Mode = enum {
             passthrough,

src/bundler/bundle_v2.zig

@@ -688,7 +688,8 @@ pub const BundleV2 = struct {
 
         if (path.pretty.ptr == path.text.ptr) {
             // TODO: outbase
-            const rel = bun.path.relativePlatform(transpiler.fs.top_level_dir, path.text, .loose, false);
+            const root_dir = if (transpiler.options.root_dir.len > 0) transpiler.options.root_dir else transpiler.fs.top_level_dir;
+            const rel = bun.path.relativePlatform(root_dir, path.text, .loose, false);
             path.pretty = bun.handleOom(this.allocator().dupe(u8, rel));
         }
         path.assertPrettyIsValid();
@@ -972,6 +973,7 @@ pub const BundleV2 = struct {
         this.linker.options.output_format = transpiler.options.output_format;
         this.linker.options.generate_bytecode_cache = transpiler.options.bytecode;
         this.linker.options.metafile = transpiler.options.metafile;
+        this.linker.options.root_dir = transpiler.options.root_dir;
 
         this.linker.dev_server = transpiler.options.dev_server;
 
@@ -3138,7 +3140,8 @@ pub const BundleV2 = struct {
     }
 
     fn pathWithPrettyInitialized(this: *BundleV2, path: Fs.Path, target: options.Target) !Fs.Path {
-        return genericPathWithPrettyInitialized(path, target, this.transpiler.fs.top_level_dir, this.allocator());
+        const root_dir = if (this.transpiler.options.root_dir.len > 0) this.transpiler.options.root_dir else this.transpiler.fs.top_level_dir;
+        return genericPathWithPrettyInitialized(path, target, root_dir, this.allocator());
     }
 
     fn reserveSourceIndexesForBake(this: *BundleV2) !void {

test/regression/issue/3039.test.ts

@@ -0,0 +1,64 @@
+import { expect, test } from "bun:test";
+import { bunEnv, bunExe, tempDir } from "harness";
+
+// Issue #3039: Filename comments in bundler output (e.g., `// src/entry.js`)
+// should be relative to the configured `root` option, not the current working directory.
+test("bundler output comments should be relative to root, not cwd", async () => {
+  using dir = tempDir("bundler-root-3039", {
+    "src/entry.js": `export const hello = "world";`,
+    "subdir/.gitkeep": "",
+  });
+
+  // Create build script with absolute paths baked in
+  const buildScript = `
+    const result = await Bun.build({
+      entrypoints: ["${String(dir)}/src/entry.js"],
+      root: "${String(dir)}",
+      minify: false,
+    });
+    console.log(await result.outputs[0].text());
+  `;
+  await Bun.write(String(dir) + "/build.js", buildScript);
+
+  // Run from root directory
+  await using procRoot = Bun.spawn({
+    cmd: [bunExe(), "build.js"],
+    cwd: String(dir),
+    env: bunEnv,
+    stderr: "pipe",
+    stdout: "pipe",
+  });
+
+  const [stdoutRoot, stderrRoot, exitCodeRoot] = await Promise.all([
+    procRoot.stdout.text(),
+    procRoot.stderr.text(),
+    procRoot.exited,
+  ]);
+
+  expect(stderrRoot).toBe("");
+  expect(stdoutRoot).toContain("// src/entry.js");
+  expect(exitCodeRoot).toBe(0);
+
+  // Run from subdir - should have the same output comment since root is set
+  await using procSubdir = Bun.spawn({
+    cmd: [bunExe(), "../build.js"],
+    cwd: String(dir) + "/subdir",
+    env: bunEnv,
+    stderr: "pipe",
+    stdout: "pipe",
+  });
+
+  const [stdoutSubdir, stderrSubdir, exitCodeSubdir] = await Promise.all([
+    procSubdir.stdout.text(),
+    procSubdir.stderr.text(),
+    procSubdir.exited,
+  ]);
+
+  expect(stderrSubdir).toBe("");
+  // The key assertion: comment should be relative to root, not cwd
+  // Before fix: would show "// ../src/entry.js" when run from subdir
+  // After fix: should show "// src/entry.js" in both cases
+  expect(stdoutSubdir).toContain("// src/entry.js");
+  expect(stdoutSubdir).not.toContain("// ../src/entry.js");
+  expect(exitCodeSubdir).toBe(0);
+});