fix: enhance tool registration and filtering for runtime-added tools

src/agent/agent.ts

@@ -263,7 +263,7 @@ export class Agent {
    * The tool becomes available to the next LLM call — no restart required.
    */
   addTool(tool: FrameworkToolDefinition): void {
-    this._toolRegistry.register(tool)
+    this._toolRegistry.register(tool, { runtimeAdded: true })
   }
 
   /**

src/agent/runner.ts

@@ -47,8 +47,6 @@ export const TOOL_PRESETS = {
   full: ['file_read', 'file_write', 'file_edit', 'grep', 'glob', 'bash'],
 } as const satisfies Record<string, readonly string[]>
 
-const BUILT_IN_TOOL_NAMES = new Set(TOOL_PRESETS.full as readonly string[])
-
 /** Framework-level disallowed tools for safety rails. */
 export const AGENT_FRAMEWORK_DISALLOWED: readonly string[] = [
   // Empty for now, infrastructure for future built-in tools
@@ -228,39 +226,40 @@ export class AgentRunner {
       )
       if (overlap.length > 0) {
         console.warn(
-          `AgentRunner: tool "${overlap[0]}" appears in both allowedTools and disallowedTools. ` +
+          `AgentRunner: tools [${overlap.map(name => `"${name}"`).join(', ')}] appear in both allowedTools and disallowedTools. ` +
           'This is contradictory and may lead to unexpected behavior.'
         )
       }
     }
 
     const allTools = this.toolRegistry.toToolDefs()
-    const customTools = allTools.filter(t => !BUILT_IN_TOOL_NAMES.has(t.name))
-    let builtInTools = allTools.filter(t => BUILT_IN_TOOL_NAMES.has(t.name))
+    const runtimeCustomTools = this.toolRegistry.toRuntimeToolDefs()
+    const runtimeCustomToolNames = new Set(runtimeCustomTools.map(t => t.name))
+    let filteredTools = allTools.filter(t => !runtimeCustomToolNames.has(t.name))
 
     // 1. Apply preset filter if set
     if (this.options.toolPreset) {
       const presetTools = new Set(TOOL_PRESETS[this.options.toolPreset] as readonly string[])
-      builtInTools = builtInTools.filter(t => presetTools.has(t.name))
+      filteredTools = filteredTools.filter(t => presetTools.has(t.name))
     }
 
     // 2. Apply allowlist filter if set
     if (this.options.allowedTools) {
-      builtInTools = builtInTools.filter(t => this.options.allowedTools!.includes(t.name))
+      filteredTools = filteredTools.filter(t => this.options.allowedTools!.includes(t.name))
     }
 
     // 3. Apply denylist filter if set
     if (this.options.disallowedTools) {
       const denied = new Set(this.options.disallowedTools)
-      builtInTools = builtInTools.filter(t => !denied.has(t.name))
+      filteredTools = filteredTools.filter(t => !denied.has(t.name))
     }
 
     // 4. Apply framework-level safety rails
     const frameworkDenied = new Set(AGENT_FRAMEWORK_DISALLOWED)
-    builtInTools = builtInTools.filter(t => !frameworkDenied.has(t.name))
+    filteredTools = filteredTools.filter(t => !frameworkDenied.has(t.name))
 
-    // Custom tools stay available regardless of built-in filtering rules.
-    return [...builtInTools, ...customTools]
+    // Runtime-added custom tools stay available regardless of filtering rules.
+    return [...filteredTools, ...runtimeCustomTools]
   }
 
   // -------------------------------------------------------------------------

src/tool/framework.ts

@@ -93,13 +93,17 @@ export function defineTool<TInput>(config: {
 export class ToolRegistry {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   private readonly tools = new Map<string, ToolDefinition<any>>()
+  private readonly runtimeToolNames = new Set<string>()
 
   /**
    * Add a tool to the registry.  Throws if a tool with the same name has
    * already been registered — prevents silent overwrites.
    */
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  register(tool: ToolDefinition<any>): void {
+  register(
+    tool: ToolDefinition<any>,
+    options?: { runtimeAdded?: boolean },
+  ): void {
     if (this.tools.has(tool.name)) {
       throw new Error(
         `ToolRegistry: a tool named "${tool.name}" is already registered. ` +
@@ -107,6 +111,9 @@ export class ToolRegistry {
       )
     }
     this.tools.set(tool.name, tool)
+    if (options?.runtimeAdded === true) {
+      this.runtimeToolNames.add(tool.name)
+    }
   }
 
   /** Return a tool by name, or `undefined` if not found. */
@@ -147,11 +154,12 @@ export class ToolRegistry {
    */
   unregister(name: string): void {
     this.tools.delete(name)
+    this.runtimeToolNames.delete(name)
   }
 
   /** Alias for {@link unregister} — available for symmetry with `register`. */
   deregister(name: string): void {
-    this.tools.delete(name)
+    this.unregister(name)
   }
 
   /**
@@ -170,6 +178,14 @@ export class ToolRegistry {
     })
   }
 
+  /**
+   * Return only tools that were added dynamically at runtime (e.g. via
+   * `agent.addTool()`), in LLM definition format.
+   */
+  toRuntimeToolDefs(): LLMToolDef[] {
+    return this.toToolDefs().filter(tool => this.runtimeToolNames.has(tool.name))
+  }
+
   /**
    * Convert all registered tools to the Anthropic-style `input_schema`
    * format.  Prefer {@link toToolDefs} for normal use; this method is exposed

tests/tool-filtering.test.ts

@@ -74,7 +74,7 @@ function createTestTools() {
     description: 'Custom tool',
     inputSchema: z.object({ input: z.string() }),
     execute: async () => ({ data: 'custom', isError: false }),
-  }))
+  }), { runtimeAdded: true })
 
   return registry
 }
@@ -248,6 +248,29 @@ describe('Tool filtering', () => {
 
       expect(toolNames).toEqual(['custom_tool'])
     })
+
+    it('runtime-added tools bypass filtering regardless of tool name', () => {
+      const runtimeBuiltinNamedRegistry = new ToolRegistry()
+      runtimeBuiltinNamedRegistry.register(defineTool({
+        name: 'file_read',
+        description: 'Runtime override',
+        inputSchema: z.object({ path: z.string() }),
+        execute: async () => ({ data: 'runtime', isError: false }),
+      }), { runtimeAdded: true })
+
+      const runtimeBuiltinNamedRunner = new AgentRunner(
+        mockAdapter,
+        runtimeBuiltinNamedRegistry,
+        new ToolExecutor(runtimeBuiltinNamedRegistry),
+        {
+          model: 'test-model',
+          disallowedTools: ['file_read'],
+        },
+      )
+
+      const tools = (runtimeBuiltinNamedRunner as any).resolveTools() as LLMToolDef[]
+      expect(tools.map(t => t.name)).toEqual(['file_read'])
+    })
   })
 
   describe('resolveTools - validation warnings', () => {
@@ -271,7 +294,7 @@ describe('Tool filtering', () => {
       ;(runner as any).resolveTools()
 
       expect(consoleWarnSpy).toHaveBeenCalledWith(
-        expect.stringContaining('tool "bash" appears in both allowedTools and disallowedTools')
+        expect.stringContaining('tools ["bash"] appear in both allowedTools and disallowedTools')
       )
     })
 
@@ -302,3 +325,4 @@ describe('Tool filtering', () => {
     })
   })
 })
+

tests/trace.test.ts

@@ -451,3 +451,4 @@ describe('Agent trace events', () => {
     expect(llmTraces[1]!.turn).toBe(2)
   })
 })
+