fix(coding-agent): use tool-name allowlists and remove cwd-bound singletons

- treat tools as a global allowlist across built-in, extension, and SDK tools
- remove process-cwd singleton tool usage from SDK and CLI paths
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/test/compaction-thinking-model.test.ts

@@ -18,7 +18,7 @@ import { AgentSession } from "../src/core/agent-session.js";
 import { ModelRegistry } from "../src/core/model-registry.js";
 import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/core/tools/index.js";
 import {
 	API_KEY,
 	createTestResourceLoader,
@@ -70,7 +70,7 @@ describe.skipIf(!HAS_ANTIGRAVITY_AUTH)("Compaction with thinking models (Antigra
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 				thinkingLevel,
 			},
 		});
@@ -168,7 +168,7 @@ describe.skipIf(!HAS_ANTHROPIC_AUTH)("Compaction with thinking models (Anthropic
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 				thinkingLevel,
 			},
 		});