diff --git a/scanners/manifest.mjs b/scanners/manifest.mjs
index 6bafe2f..1940076 100644
--- a/scanners/manifest.mjs
+++ b/scanners/manifest.mjs
@@ -171,19 +171,26 @@ export function summarizeByLoadPattern(sources) {
 /**
  * Source strings (the `source` field buildManifest stamps) that belong to the
  * SHARED GLOBAL layer — config paid once per machine and identical in every
- * repo: the global ~/.claude CLAUDE.md, managed enterprise policy, and the
- * global MCP slice of ~/.claude.json. Installed plugins are also shared but are
- * matched by the `plugin:` prefix below, not by this set.
+ * repo: the global ~/.claude CLAUDE.md (`user`) and managed enterprise policy
+ * (`managed`). Installed plugins are also shared but are matched by the
+ * `plugin:` prefix below, not by this set.
+ *
+ * Deliberately NOT here: `~/.claude.json:projects`. Although that file lives in
+ * HOME, `readClaudeJsonProjectSlice` returns the slice keyed to the SPECIFIC
+ * repo path — those MCP servers are per-repo, load only in their own project,
+ * and differ across repos, so they are a delta (folding them into the
+ * once-counted shared layer would drop every repo's slice but the first). The
+ * only machine-global MCP is plugin-provided (caught by the `plugin:` prefix).
  */
-const SHARED_GLOBAL_SOURCES = Object.freeze(new Set(['user', 'managed', '~/.claude.json:projects']));
+const SHARED_GLOBAL_SOURCES = Object.freeze(new Set(['user', 'managed']));
 
 /**
  * Classify one manifest source as part of the once-counted shared global layer
  * or a per-repo delta (v5.9 B2b). Anything not positively identified as global
- * (project / local / .mcp.json / @import / unrecognized) falls to `delta`, so a
- * source is never silently folded into the shared layer — a wrong fold would
- * HIDE machine-wide cost, whereas a wrong delta is at worst attributed visibly
- * to a repo.
+ * (project / local / .mcp.json / ~/.claude.json:projects / @import / unrecognized)
+ * falls to `delta`, so a source is never silently folded into the shared layer —
+ * a wrong fold would HIDE machine-wide cost, whereas a wrong delta is at worst
+ * attributed visibly to a repo.
  * @param {string} source
  * @returns {'shared'|'delta'}
  */
diff --git a/tests/scanners/manifest.test.mjs b/tests/scanners/manifest.test.mjs
index d2ca618..cd0da1a 100644
--- a/tests/scanners/manifest.test.mjs
+++ b/tests/scanners/manifest.test.mjs
@@ -203,11 +203,12 @@ describe('splitManifestByOwnership — shared-global vs per-repo-delta (unit, v5
     assert.equal(classifyOwnership('user'), 'shared');
     assert.equal(classifyOwnership('managed'), 'shared');
     assert.equal(classifyOwnership('plugin:foo'), 'shared');
-    assert.equal(classifyOwnership('~/.claude.json:projects'), 'shared');
     // Per-repo delta: the repo's own project/local contribution.
     assert.equal(classifyOwnership('project'), 'delta');
     assert.equal(classifyOwnership('local'), 'delta');
     assert.equal(classifyOwnership('.mcp.json'), 'delta');
+    // ~/.claude.json:projects is a per-repo MCP slice (keyed by repo path), NOT shared.
+    assert.equal(classifyOwnership('~/.claude.json:projects'), 'delta');
     // import + anything unrecognized → delta (never silently folded into the shared layer).
     assert.equal(classifyOwnership('import'), 'delta');
     assert.equal(classifyOwnership('mystery'), 'delta');
@@ -218,7 +219,7 @@ describe('splitManifestByOwnership — shared-global vs per-repo-delta (unit, v5
     src('user', 'always', 100), // global CLAUDE.md → shared
     src('managed', 'always', 50), // managed policy → shared
     src('plugin:foo', 'always', 30), // plugin agent/rule → shared
-    src('~/.claude.json:projects', 'always', 20), // global MCP → shared
+    src('~/.claude.json:projects', 'always', 20), // per-repo MCP slice → delta
     src('project', 'always', 10), // project CLAUDE.md/rule → delta
     src('local', 'always', 5), // local → delta
     src('.mcp.json', 'always', 7), // project MCP → delta
@@ -226,14 +227,14 @@ describe('splitManifestByOwnership — shared-global vs per-repo-delta (unit, v5
   ];
   const { shared, delta } = splitManifestByOwnership(sources);
 
-  it('folds global/user/managed/plugin/global-MCP into the shared layer', () => {
-    assert.equal(shared.always.tokens, 100 + 50 + 30 + 20); // 200
-    assert.equal(shared.always.count, 4);
+  it('folds global/user/managed/plugin into the shared layer', () => {
+    assert.equal(shared.always.tokens, 100 + 50 + 30); // 180
+    assert.equal(shared.always.count, 3);
   });
 
-  it('attributes project/local/.mcp.json/import to the per-repo delta', () => {
-    assert.equal(delta.always.tokens, 10 + 5 + 7 + 3); // 25
-    assert.equal(delta.always.count, 4);
+  it('attributes project/local/.mcp.json/claude.json-slice/import to the per-repo delta', () => {
+    assert.equal(delta.always.tokens, 20 + 10 + 5 + 7 + 3); // 45
+    assert.equal(delta.always.count, 5);
   });
 
   it('preserves load-pattern buckets within each layer', () => {