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

- switch SDK/CLI tool selection to name-based allowlists
- apply allowlists across built-in, extension, and SDK tools
- remove ambient process.cwd defaults from core tooling and resource helpers
- update tests, examples, and TUI callers for explicit cwd plumbing
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/src/index.ts

@@ -183,8 +183,6 @@ export {
 	createReadTool,
 	createWriteTool,
 	type PromptTemplate,
-	// Pre-built tools (use process.cwd())
-	readOnlyTools,
 } from "./core/sdk.js";
 export {
 	type BranchSummaryEntry,
@@ -235,9 +233,6 @@ export {
 	type BashToolDetails,
 	type BashToolInput,
 	type BashToolOptions,
-	bashTool,
-	bashToolDefinition,
-	codingTools,
 	createBashToolDefinition,
 	createEditToolDefinition,
 	createFindToolDefinition,
@@ -252,33 +247,23 @@ export {
 	type EditToolDetails,
 	type EditToolInput,
 	type EditToolOptions,
-	editTool,
-	editToolDefinition,
 	type FindOperations,
 	type FindToolDetails,
 	type FindToolInput,
 	type FindToolOptions,
-	findTool,
-	findToolDefinition,
 	formatSize,
 	type GrepOperations,
 	type GrepToolDetails,
 	type GrepToolInput,
 	type GrepToolOptions,
-	grepTool,
-	grepToolDefinition,
 	type LsOperations,
 	type LsToolDetails,
 	type LsToolInput,
 	type LsToolOptions,
-	lsTool,
-	lsToolDefinition,
 	type ReadOperations,
 	type ReadToolDetails,
 	type ReadToolInput,
 	type ReadToolOptions,
-	readTool,
-	readToolDefinition,
 	type ToolsOptions,
 	type TruncationOptions,
 	type TruncationResult,
@@ -289,8 +274,6 @@ export {
 	type WriteToolInput,
 	type WriteToolOptions,
 	withFileMutationQueue,
-	writeTool,
-	writeToolDefinition,
 } from "./core/tools/index.js";
 // Main entry point
 export { type MainOptions, main } from "./main.js";