diff --git a/packages/core/src/__tests__/config-validation.test.ts b/packages/core/src/__tests__/config-validation.test.ts
index 2703154e7..be7f9a0a2 100644
--- a/packages/core/src/__tests__/config-validation.test.ts
+++ b/packages/core/src/__tests__/config-validation.test.ts
@@ -1032,4 +1032,22 @@ describe("External Plugin Name Generation", () => {
 
     expect(config.projects.proj1.tracker?.plugin).toBe("my-custom-name");
   });
+
+  it("handles local path without slashes correctly", () => {
+    const config = validateConfig({
+      projects: {
+        proj1: {
+          path: "/repos/test",
+          repo: "org/test",
+          defaultBranch: "main",
+          tracker: {
+            path: "my-tracker",
+          },
+        },
+      },
+    });
+
+    // Should use the path as-is (not split by hyphens like npm packages)
+    expect(config.projects.proj1.tracker?.plugin).toBe("my-tracker");
+  });
 });
diff --git a/packages/core/src/__tests__/plugin-registry.test.ts b/packages/core/src/__tests__/plugin-registry.test.ts
index b34907b73..424492ab5 100644
--- a/packages/core/src/__tests__/plugin-registry.test.ts
+++ b/packages/core/src/__tests__/plugin-registry.test.ts
@@ -535,14 +535,13 @@ describe("External plugin manifest validation", () => {
     });
 
     // Should warn but not throw (error is caught and logged)
-    const consoleSpy = vi.spyOn(console, "warn").mockImplementation(() => {});
+    const stderrSpy = vi.spyOn(process.stderr, "write").mockImplementation(() => true);
     await registry.loadFromConfig(config, importFn);
 
-    expect(consoleSpy).toHaveBeenCalledWith(
+    expect(stderrSpy).toHaveBeenCalledWith(
       expect.stringContaining("Failed to load plugin"),
-      expect.any(Error),
     );
-    consoleSpy.mockRestore();
+    stderrSpy.mockRestore();
   });
 
   it("infers plugin name when expectedPluginName is not specified", async () => {
@@ -671,12 +670,73 @@ describe("External plugin manifest validation", () => {
       ],
     });
 
-    const consoleSpy = vi.spyOn(console, "warn").mockImplementation(() => {});
+    const stderrSpy = vi.spyOn(process.stderr, "write").mockImplementation(() => true);
     await registry.loadFromConfig(config, importFn);
 
-    expect(consoleSpy).toHaveBeenCalledWith(
+    expect(stderrSpy).toHaveBeenCalledWith(
       expect.stringContaining("has slot \"notifier\" but was configured as \"tracker\""),
     );
-    consoleSpy.mockRestore();
+    stderrSpy.mockRestore();
+  });
+
+  it("updates all projects sharing same external plugin with manifest.name", async () => {
+    const registry = createPluginRegistry();
+
+    const mockPlugin = {
+      manifest: { name: "jira-cloud", slot: "tracker" as const, version: "1.0.0", description: "Jira Cloud" },
+      create: vi.fn(() => ({})),
+    };
+
+    const importFn = vi.fn(async () => mockPlugin);
+
+    const config = makeOrchestratorConfig({
+      configPath: "/test/config.yaml",
+      plugins: [
+        { name: "jira", source: "npm", package: "@acme/ao-plugin-tracker-jira", enabled: true },
+      ],
+      projects: {
+        proj1: {
+          path: "/repos/test1",
+          repo: "org/test1",
+          name: "proj1",
+          defaultBranch: "main",
+          sessionPrefix: "test1",
+          tracker: { plugin: "jira", package: "@acme/ao-plugin-tracker-jira" },
+        },
+        proj2: {
+          path: "/repos/test2",
+          repo: "org/test2",
+          name: "proj2",
+          defaultBranch: "main",
+          sessionPrefix: "test2",
+          // Same external plugin as proj1
+          tracker: { plugin: "jira", package: "@acme/ao-plugin-tracker-jira" },
+        },
+      },
+      _externalPluginEntries: [
+        {
+          source: "projects.proj1.tracker",
+          location: { kind: "project", projectId: "proj1", configType: "tracker" },
+          slot: "tracker",
+          package: "@acme/ao-plugin-tracker-jira",
+          // No expectedPluginName - will accept any manifest.name
+        },
+        {
+          source: "projects.proj2.tracker",
+          location: { kind: "project", projectId: "proj2", configType: "tracker" },
+          slot: "tracker",
+          package: "@acme/ao-plugin-tracker-jira",
+          // No expectedPluginName - will accept any manifest.name
+        },
+      ],
+    });
+
+    await registry.loadFromConfig(config, importFn);
+
+    // Both projects should be updated with the actual manifest.name
+    expect(config.projects.proj1.tracker?.plugin).toBe("jira-cloud");
+    expect(config.projects.proj2.tracker?.plugin).toBe("jira-cloud");
+    // Plugin should be registered under manifest.name
+    expect(registry.get("tracker", "jira-cloud")).not.toBeNull();
   });
 });
diff --git a/packages/core/src/config.ts b/packages/core/src/config.ts
index 387e493be..7c09a23f9 100644
--- a/packages/core/src/config.ts
+++ b/packages/core/src/config.ts
@@ -313,22 +313,26 @@ function expandPaths(config: OrchestratorConfig): OrchestratorConfig {
  * Format: extract the last segment from the package/path, removing common prefixes.
  * e.g., "@acme/ao-plugin-tracker-jira" -> "jira"
  * e.g., "./plugins/my-tracker" -> "my-tracker"
+ * e.g., "my-tracker" (local path without slashes) -> "my-tracker"
  */
 function generateTempPluginName(pkg?: string, path?: string): string {
-  const specifier = pkg ?? path ?? "unknown";
-
-  // For npm packages, extract the last part after the last hyphen or slash
+  // Handle npm packages: extract the last part after the last hyphen
   // @acme/ao-plugin-tracker-jira -> jira
   // @composio/ao-plugin-scm-gitlab -> gitlab
-  if (specifier.startsWith("@") || !specifier.includes("/")) {
-    const parts = specifier.split(/[-/]/);
-    return parts[parts.length - 1] ?? specifier;
+  if (pkg) {
+    const parts = pkg.split(/[-/]/);
+    return parts[parts.length - 1] ?? pkg;
   }
 
-  // For local paths, use the basename
+  // Handle local paths: use the basename
   // ./plugins/my-tracker -> my-tracker
-  const segments = specifier.split("/").filter((s) => s && s !== "." && s !== "..");
-  return segments[segments.length - 1] ?? specifier;
+  // my-tracker -> my-tracker (no slashes is still a valid path)
+  if (path) {
+    const segments = path.split("/").filter((s) => s && s !== "." && s !== "..");
+    return segments[segments.length - 1] ?? path;
+  }
+
+  return "unknown";
 }
 
 /**
diff --git a/packages/core/src/plugin-registry.ts b/packages/core/src/plugin-registry.ts
index 9812e355d..6d5793f70 100644
--- a/packages/core/src/plugin-registry.ts
+++ b/packages/core/src/plugin-registry.ts
@@ -86,16 +86,20 @@ function extractPluginConfig(
 }
 
 /**
- * Find the external plugin entry that matches a given plugin config.
+ * Find ALL external plugin entries that match a given plugin config.
  * Used for manifest.name validation when loading inline tracker/scm/notifier plugins.
+ *
+ * Returns all matching entries because multiple projects may share the same
+ * external plugin (same package/path), and all their configs need to be updated
+ * with the actual manifest.name.
  */
-function findExternalPluginEntry(
+function findAllExternalPluginEntries(
   plugin: InstalledPluginConfig,
   externalEntries: ExternalPluginEntryRef[] | undefined,
-): ExternalPluginEntryRef | undefined {
-  if (!externalEntries) return undefined;
+): ExternalPluginEntryRef[] {
+  if (!externalEntries) return [];
 
-  return externalEntries.find((entry) => {
+  return externalEntries.filter((entry) => {
     if (plugin.package && entry.package === plugin.package) return true;
     if (plugin.path && entry.path === plugin.path) return true;
     return false;
@@ -153,9 +157,9 @@ function updateConfigWithManifestName(
 
   // Also validate slot matches
   if (manifest.slot !== slot) {
-    console.warn(
+    process.stderr.write(
       `[plugin-registry] Plugin at ${source} has slot "${manifest.slot}" but was configured as "${slot}". ` +
-        `The plugin will be registered under its declared slot "${manifest.slot}".`,
+        `The plugin will be registered under its declared slot "${manifest.slot}".\n`,
     );
   }
 }
@@ -344,7 +348,7 @@ export function createPluginRegistry(): PluginRegistry {
 
         const specifier = resolvePluginSpecifier(plugin, config);
         if (!specifier) {
-          console.warn(`[plugin-registry] Could not resolve specifier for plugin "${plugin.name}" (source: ${plugin.source})`);
+          process.stderr.write(`[plugin-registry] Could not resolve specifier for plugin "${plugin.name}" (source: ${plugin.source})\n`);
           continue;
         }
 
@@ -353,8 +357,9 @@ export function createPluginRegistry(): PluginRegistry {
           if (!mod) continue;
 
           // Check if this plugin was auto-added from inline tracker/scm/notifier config
-          const externalEntry = findExternalPluginEntry(plugin, externalEntries);
-          if (externalEntry) {
+          // Multiple projects may share the same external plugin, so find ALL matching entries
+          const matchingEntries = findAllExternalPluginEntries(plugin, externalEntries);
+          for (const externalEntry of matchingEntries) {
             // Validate manifest.name matches expectedPluginName (if specified)
             validateManifestName(mod.manifest, externalEntry, specifier);
             // Update the config with the actual manifest.name
@@ -364,7 +369,7 @@ export function createPluginRegistry(): PluginRegistry {
           const pluginConfig = extractPluginConfig(mod.manifest.slot, mod.manifest.name, config);
           this.register(mod, pluginConfig);
         } catch (error) {
-          console.warn(`[plugin-registry] Failed to load plugin "${specifier}":`, error);
+          process.stderr.write(`[plugin-registry] Failed to load plugin "${specifier}": ${error}\n`);
         }
       }
     },