diff --git a/src/commands/manifest/generate-recursive-manifests.mts b/src/commands/manifest/generate-recursive-manifests.mts
index 979184f60..ca3246cd9 100644
--- a/src/commands/manifest/generate-recursive-manifests.mts
+++ b/src/commands/manifest/generate-recursive-manifests.mts
@@ -134,7 +134,10 @@ export function resolveEcosystemConfig(
 // root under `cwd`. Coverage is tracked per ecosystem via the facts SBOM's
 // own projects[].subprojectDir, not by pruning the whole discovered subtree,
 // so an unrelated nested project a reactor doesn't declare still gets its
-// own invocation. Fail-closed per ecosystem, not globally: a root whose
+// own invocation - and only a properly nested subprojectDir counts as
+// coverage at all; one that escapes its declaring reactor's own directory
+// still gets its own independent invocation too (see the covered.add call
+// below). Fail-closed per ecosystem, not globally: a root whose
 // workspace layout can't be determined aborts only that ecosystem's own
 // remaining walk (marking its untried candidates 'aborted'), since coverage
 // is tracked per ecosystem and an unrelated one has nothing to lose from it.
@@ -242,7 +245,20 @@ export async function generateRecursiveManifests({
         ),
       )
       for (const subprojectDir of resolvedSubprojectDirs) {
-        covered.add(subprojectDir)
+        // Only a genuinely nested member (a descendant of this reactor's own
+        // directory) has no independent existence worth its own standalone
+        // analysis. A subprojectDir that escapes this reactor's own tree (a
+        // sibling, e.g. Maven's `<module>../shared-lib</module>` or Gradle's
+        // relocated projectDir) is independently locatable and potentially
+        // independently consumed or published - its own un-mediated
+        // resolution (e.g. a dependency version this reactor's own
+        // dependency management happens to override) is a distinct,
+        // meaningful data point, not a redundant one. Never suppress its own
+        // build-root invocation, regardless of which reactor(s) also
+        // incorporate it or the order candidates happen to be discovered in.
+        if (subprojectDir.startsWith(`${dir}${path.sep}`)) {
+          covered.add(subprojectDir)
+        }
       }
       outcomes.push({
         dir,
diff --git a/src/commands/manifest/generate-recursive-manifests.test.mts b/src/commands/manifest/generate-recursive-manifests.test.mts
index 8f4cb97ca..e81d65bab 100644
--- a/src/commands/manifest/generate-recursive-manifests.test.mts
+++ b/src/commands/manifest/generate-recursive-manifests.test.mts
@@ -106,6 +106,67 @@ describe('generateRecursiveManifests', () => {
     )
   })
 
+  it.each([
+    // Escaping references must get their own independent invocation
+    // regardless of where they happen to sort alphabetically relative to the
+    // reactor that declares them - before ('aaa-shared-lib') and after
+    // ('zzz-shared-lib') both have to behave identically.
+    ['aaa-shared-lib'],
+    ['zzz-shared-lib'],
+  ])(
+    'never suppresses a sibling subprojectDir that escapes its declaring reactor (name: %s)',
+    async sharedLibName => {
+      const outer = await fs.realpath(
+        await fs.mkdtemp(path.join(tmpdir(), 'escaping-subproject-')),
+      )
+      const reactorA = path.join(outer, 'reactor-a')
+      const sharedLib = path.join(outer, sharedLibName)
+      try {
+        await fs.mkdir(reactorA, { recursive: true })
+        await fs.mkdir(sharedLib, { recursive: true })
+        await fs.writeFile(path.join(reactorA, 'pom.xml'), '<project/>')
+        await fs.writeFile(path.join(sharedLib, 'pom.xml'), '<project/>')
+
+        vi.mocked(runManifestFacts).mockImplementation(async ({ cwd }) => {
+          if (cwd === reactorA) {
+            return {
+              factsPath: path.join(cwd, '.socket.facts.json'),
+              projects: [
+                {
+                  type: 'maven',
+                  name: 'shared-lib',
+                  subprojectDir: `../${sharedLibName}`,
+                  dependencies: [],
+                  resolvedAs: [],
+                },
+              ],
+            }
+          }
+          return {
+            factsPath: path.join(cwd, '.socket.facts.json'),
+            projects: [],
+          }
+        })
+
+        const outcomes = await generateRecursiveManifests({
+          cwd: outer,
+          verbose: false,
+        })
+
+        const byDir = new Map(outcomes.map(o => [o.dir, o.status]))
+        expect(byDir.get(reactorA)).toBe('generated')
+        expect(byDir.get(sharedLib)).toBe('generated')
+        expect(
+          vi
+            .mocked(runManifestFacts)
+            .mock.calls.some(([opts]) => opts.cwd === sharedLib),
+        ).toBe(true)
+      } finally {
+        await fs.rm(outer, { recursive: true, force: true })
+      }
+    },
+  )
+
   it("runs both ecosystems unconditionally at a dual-marker directory (matches auto's existing behavior)", async () => {
     vi.mocked(runManifestFacts).mockImplementation(async ({ cwd }) => ({
       factsPath: path.join(cwd, '.socket.facts.json'),
diff --git a/src/commands/manifest/setup-recursive-manifest-config.mts b/src/commands/manifest/setup-recursive-manifest-config.mts
index 62ccc0617..a82ede0fe 100644
--- a/src/commands/manifest/setup-recursive-manifest-config.mts
+++ b/src/commands/manifest/setup-recursive-manifest-config.mts
@@ -192,12 +192,14 @@ export async function discoverBuildRoots({
 // Enumerates one build root's declared workspace members (see
 // enumerate-workspaces.mts) and folds them into `coveredByEcosystem`, so a
 // later candidate matching one is recognized as a reactor member rather than
-// independent. Called per-candidate right after its own prompt, not as a
-// bulk pass, so the build invocation never blocks candidates that don't need
-// it. A disabled candidate is skipped (no point invoking an off build tool);
-// otherwise this fails closed, same reasoning as generateRecursiveManifests -
-// if enumeration fails there's no way to tell covered from independent, so
-// the caller aborts rather than guess.
+// independent - only a properly nested subprojectDir counts as coverage at
+// all; one that escapes this candidate's own directory still gets its own
+// entry (see the set.add call below). Called per-candidate right after its
+// own prompt, not as a bulk pass, so the build invocation never blocks
+// candidates that don't need it. A disabled candidate is skipped (no point
+// invoking an off build tool); otherwise this fails closed, same reasoning
+// as generateRecursiveManifests - if enumeration fails there's no way to
+// tell covered from independent, so the caller aborts rather than guess.
 export async function markWorkspaceCoverage({
   candidate,
   coveredByEcosystem,
@@ -251,7 +253,15 @@ export async function markWorkspaceCoverage({
     ),
   )
   for (const subprojectDir of resolvedSubprojectDirs) {
-    set.add(subprojectDir)
+    // Only a genuinely nested member (a descendant of this candidate's own
+    // directory) should be skipped as covered by it. A subprojectDir that
+    // escapes this candidate's own tree (a sibling, e.g. Maven's
+    // `<module>../shared-lib</module>` or Gradle's relocated projectDir) is
+    // independently locatable and worth its own socket.json entry - never
+    // mark it covered, regardless of which candidate(s) also incorporate it.
+    if (subprojectDir.startsWith(`${candidate.dir}${path.sep}`)) {
+      set.add(subprojectDir)
+    }
   }
   coveredByEcosystem.set(candidate.ecosystem, set)
   return { ok: true, data: undefined }
diff --git a/src/commands/manifest/setup-recursive-manifest-config.test.mts b/src/commands/manifest/setup-recursive-manifest-config.test.mts
index 0e7d53ea9..c96e0750a 100644
--- a/src/commands/manifest/setup-recursive-manifest-config.test.mts
+++ b/src/commands/manifest/setup-recursive-manifest-config.test.mts
@@ -266,6 +266,42 @@ describe('markWorkspaceCoverage', () => {
     )
   })
 
+  it('does not mark a sibling subprojectDir that escapes the candidate directory as covered', async () => {
+    vi.mocked(enumerateWorkspaces).mockResolvedValue({
+      projects: [
+        {
+          type: 'maven',
+          name: 'moduleA',
+          subprojectDir: 'moduleA',
+          dependencies: [],
+          resolvedAs: [],
+        },
+        {
+          type: 'maven',
+          name: 'shared-lib',
+          subprojectDir: '../shared-lib',
+          dependencies: [],
+          resolvedAs: [],
+        },
+      ],
+    })
+    const coveredByEcosystem = new Map<BuildTool, Set<string>>()
+
+    await markWorkspaceCoverage({
+      candidate: { dir: reactor, ecosystem: 'maven' },
+      coveredByEcosystem,
+      cwd,
+      rootSockJson: emptySockJson(),
+    })
+
+    expect(coveredByEcosystem.get('maven')).toEqual(
+      new Set([reactor, `${reactor}/moduleA`]),
+    )
+    expect(coveredByEcosystem.get('maven')?.has(`${cwd}/shared-lib`)).toBe(
+      false,
+    )
+  })
+
   it('does not enumerate, and marks nothing covered, for a disabled candidate', async () => {
     vi.mocked(readSocketJsonCascade).mockReturnValue({
       version: 1,