diff --git a/packages/server/src/server/project-group-key.test.ts b/packages/server/src/server/project-group-key.test.ts
index 6be6120e5..a7f79dcd2 100644
--- a/packages/server/src/server/project-group-key.test.ts
+++ b/packages/server/src/server/project-group-key.test.ts
@@ -29,6 +29,19 @@ describe("deriveProjectGroupKey", () => {
     ).toBe("remote:git.example.com/repo");
   });
 
+  test("accepts an SCP-style remote without a username", () => {
+    const rootPath = path.resolve("repo");
+
+    expect(
+      deriveProjectGroupKey({
+        rootPath,
+        remoteUrl: "github.com:getpaseo/paseo.git",
+        worktreeRoot: rootPath,
+        mainRepoRoot: null,
+      }),
+    ).toBe("remote:github.com/getpaseo/paseo");
+  });
+
   test("includes the selected path within a repository", () => {
     const worktreeRoot = path.resolve("repo");
     const rootPath = path.join(worktreeRoot, "packages", "app");
diff --git a/packages/server/src/server/project-group-key.ts b/packages/server/src/server/project-group-key.ts
index 81dbfa7db..7f554a178 100644
--- a/packages/server/src/server/project-group-key.ts
+++ b/packages/server/src/server/project-group-key.ts
@@ -38,7 +38,10 @@ function deriveRemoteProjectGroupKey(remoteUrl: string | null): string | null {
 
   let host: string | null = null;
   let remotePath: string | null = null;
-  const scpLike = trimmed.match(/^[^@]+@([^:]+):(.+)$/);
+  const scpLike =
+    !trimmed.includes("://") && !/^[A-Za-z]:[\\/]/.test(trimmed)
+      ? trimmed.match(/^(?:[^@/:]+@)?([^/:]+):(.+)$/)
+      : null;
   if (scpLike) {
     host = scpLike[1] ?? null;
     remotePath = scpLike[2] ?? null;
diff --git a/packages/server/src/server/workspace-registry-bootstrap-legacy.ts b/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
index c3bf8736f..e1cea95ad 100644
--- a/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
+++ b/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
@@ -1,4 +1,4 @@
-import { basename, resolve } from "node:path";
+import { basename, isAbsolute, relative, resolve, sep } from "node:path";
 
 import type { ProjectCheckoutLitePayload } from "@getpaseo/protocol/messages";
 
@@ -75,7 +75,20 @@ function deriveProjectRootPath(input: {
   cwd: string;
   checkout: ProjectCheckoutLitePayload;
 }): string {
-  return input.checkout.isGit && input.checkout.mainRepoRoot
-    ? input.checkout.mainRepoRoot
-    : input.cwd;
+  if (!input.checkout.isGit || !input.checkout.mainRepoRoot) return input.cwd;
+  const worktreeRoot = input.checkout.worktreeRoot
+    ? parseGitRevParsePath(input.checkout.worktreeRoot)
+    : null;
+  if (!worktreeRoot) return input.checkout.mainRepoRoot;
+  const selectedPath = relative(resolve(worktreeRoot), resolve(input.cwd));
+  if (
+    !selectedPath ||
+    selectedPath === "." ||
+    selectedPath === ".." ||
+    selectedPath.startsWith(`..${sep}`) ||
+    isAbsolute(selectedPath)
+  ) {
+    return input.checkout.mainRepoRoot;
+  }
+  return resolve(input.checkout.mainRepoRoot, selectedPath);
 }
diff --git a/packages/server/src/server/workspace-registry-bootstrap.test.ts b/packages/server/src/server/workspace-registry-bootstrap.test.ts
index 033fdc6dc..f4c3a1ca1 100644
--- a/packages/server/src/server/workspace-registry-bootstrap.test.ts
+++ b/packages/server/src/server/workspace-registry-bootstrap.test.ts
@@ -378,8 +378,8 @@ describe("bootstrapWorkspaceRegistries", () => {
   });
 
   test("keeps legacy agents in different monorepo subprojects separate", async () => {
-    const appProject = path.join(GIT_PROJECT, "packages", "app");
-    const serverProject = path.join(GIT_PROJECT, "packages", "server");
+    const appProject = path.join(GIT_WORKTREE, "packages", "app");
+    const serverProject = path.join(GIT_WORKTREE, "packages", "server");
     mkdirSync(appProject, { recursive: true });
     mkdirSync(serverProject, { recursive: true });
     workspaceGitService = createNoopWorkspaceGitService({
@@ -388,9 +388,9 @@ describe("bootstrapWorkspaceRegistries", () => {
         isGit: true,
         currentBranch: "main",
         remoteUrl: "git@github.com:acme/legacy-project.git",
-        worktreeRoot: GIT_PROJECT,
+        worktreeRoot: GIT_WORKTREE,
         isPaseoOwnedWorktree: false,
-        mainRepoRoot: null,
+        mainRepoRoot: GIT_PROJECT,
       }),
     });
     await agentStorage.initialize();
@@ -428,16 +428,22 @@ describe("bootstrapWorkspaceRegistries", () => {
 
     expect(
       (await projectRegistry.list())
-        .map((project) => ({ projectId: project.projectId, displayName: project.displayName }))
+        .map((project) => ({
+          projectId: project.projectId,
+          displayName: project.displayName,
+          rootPath: project.rootPath,
+        }))
         .sort((left, right) => left.projectId.localeCompare(right.projectId)),
     ).toEqual([
       {
         projectId: "remote:github.com/acme/legacy-project#subdir:packages/app",
         displayName: "app",
+        rootPath: path.join(GIT_PROJECT, "packages", "app"),
       },
       {
         projectId: "remote:github.com/acme/legacy-project#subdir:packages/server",
         displayName: "server",
+        rootPath: path.join(GIT_PROJECT, "packages", "server"),
       },
     ]);
     expect(