fix(ego-lint): deduplicate prototype-override warnings (#32)

## Summary

Field test #10 (Just Perfection) revealed that the prototype-override
detection regex `\w+\.prototype\.\w+\s*=` matches both the override and
the restore, causing each prototype to appear twice (5 warnings for 3
unique prototypes).

- Deduplicate `prototype_overrides` by `(file, prototype_name)` before
emitting warnings

Closes #28

## Test plan

- [x] New fixture `proto-override-dedup@test` with override + restore
pattern
- [x] Verifies 2 unique warnings (not 4) for 2 prototypes
- [x] 454 tests pass (452 baseline + 2 new)
- [x] Verify no regressions on other field-tested extensions

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: ZviBaratz

skills/ego-lint/scripts/check-lifecycle.py

@@ -374,15 +374,23 @@ def check_injection_manager(ext_dir):
 
     # WS1-D: Detect direct prototype overrides
     prototype_overrides = []
+    seen_overrides = set()
     for filepath in js_files:
         content = strip_comments(read_file(filepath))
         rel = os.path.relpath(filepath, ext_dir)
         # SomeClass.prototype.methodName = ...
         for m in re.finditer(r'(\w+\.prototype\.\w+)\s*=', content):
-            prototype_overrides.append((rel, m.group(1)))
+            key = (rel, m.group(1))
+            if key not in seen_overrides:
+                seen_overrides.add(key)
+                prototype_overrides.append(key)
         # Object.assign(SomeClass.prototype, ...)
         for m in re.finditer(r'Object\.assign\s*\(\s*(\w+\.prototype)', content):
-            prototype_overrides.append((rel, f"Object.assign({m.group(1)}, ...)"))
+            label = f"Object.assign({m.group(1)}, ...)"
+            key = (rel, label)
+            if key not in seen_overrides:
+                seen_overrides.add(key)
+                prototype_overrides.append(key)
 
     if prototype_overrides:
         # Check if disable() restores prototypes

tests/assertions/proto-override-dedup.sh

@@ -0,0 +1,9 @@
+# Field test #10: prototype-override deduplication (closes #28)
+
+# --- proto-override-dedup (each prototype warned only once) ---
+echo "=== proto-override-dedup ==="
+run_lint "proto-override-dedup@test"
+assert_output_contains "prototype override detected" "\[WARN\].*lifecycle/prototype-override.*BackgroundMenu.prototype.open"
+assert_output_contains "search prototype override detected" "\[WARN\].*lifecycle/prototype-override.*SearchController.prototype.startSearch"
+assert_output_count "exactly 2 prototype-override warnings (dedup works)" "\[WARN\].*lifecycle/prototype-override" 2
+echo ""

tests/fixtures/proto-override-dedup@test/LICENSE

@@ -0,0 +1 @@
+SPDX-License-Identifier: GPL-2.0-or-later

tests/fixtures/proto-override-dedup@test/extension.js

@@ -0,0 +1,14 @@
+import {Extension} from 'resource:///org/gnome/shell/extensions/extension.js';
+import {API} from './lib/api.js';
+
+export default class TestExtension extends Extension {
+    enable() {
+        this._api = new API();
+        this._api.open();
+    }
+
+    disable() {
+        this._api.close();
+        this._api = null;
+    }
+}

tests/fixtures/proto-override-dedup@test/lib/api.js

@@ -0,0 +1,21 @@
+import * as BackgroundMenu from 'resource:///org/gnome/shell/ui/backgroundMenu.js';
+import * as Search from 'resource:///org/gnome/shell/ui/search.js';
+
+export class API {
+    #originals = {};
+
+    open() {
+        // Override prototype — saves original first
+        this.#originals['bgOpen'] = BackgroundMenu.BackgroundMenu.prototype.open;
+        BackgroundMenu.BackgroundMenu.prototype.open = () => {};
+
+        this.#originals['startSearch'] = Search.SearchController.prototype.startSearch;
+        Search.SearchController.prototype.startSearch = () => {};
+    }
+
+    close() {
+        // Restore originals
+        BackgroundMenu.BackgroundMenu.prototype.open = this.#originals['bgOpen'];
+        Search.SearchController.prototype.startSearch = this.#originals['startSearch'];
+    }
+}

tests/fixtures/proto-override-dedup@test/metadata.json

@@ -0,0 +1,7 @@
+{
+    "uuid": "proto-override-dedup@test",
+    "name": "Test Proto Override Dedup",
+    "description": "Tests that prototype override warnings are deduplicated",
+    "shell-version": ["48"],
+    "url": "https://example.com"
+}

tests/run-tests.sh

@@ -45,6 +45,19 @@ assert_exit_code() {
     fi
 }
 
+assert_output_count() {
+    local label="$1" pattern="$2" expected="$3"
+    local actual
+    actual=$(echo "$output" | grep -cE "$pattern" || true)
+    if [[ "$actual" -eq "$expected" ]]; then
+        echo -e "  ${GREEN}✓${NC} $label (count: $actual)"
+        PASS_COUNT=$((PASS_COUNT + 1))
+    else
+        echo -e "  ${RED}✗${NC} $label (expected $expected matches, got $actual)"
+        FAIL_COUNT=$((FAIL_COUNT + 1))
+    fi
+}
+
 run_lint() {
     local fixture="$1"
     output=""