fix: update filtering logic to allow custom tools

README.md

@@ -199,19 +199,19 @@ Predefined tool sets for common use cases:
 const readonlyAgent: AgentConfig = {
   name: 'reader',
   model: 'claude-sonnet-4-6',
-  toolPreset: 'readonly',  // file_read, grep
+  toolPreset: 'readonly',  // file_read, grep, glob
 }
 
 const readwriteAgent: AgentConfig = {
   name: 'editor',
   model: 'claude-sonnet-4-6',
-  toolPreset: 'readwrite',  // file_read, file_write, file_edit, grep
+  toolPreset: 'readwrite',  // file_read, file_write, file_edit, grep, glob
 }
 
 const fullAgent: AgentConfig = {
   name: 'executor',
   model: 'claude-sonnet-4-6',
-  toolPreset: 'full',  // all built-in tools including bash
+  toolPreset: 'full',  // file_read, file_write, file_edit, grep, glob, bash
 }
 ```
 
@@ -223,7 +223,7 @@ Combine presets with allowlists and denylists for precise control:
 const customAgent: AgentConfig = {
   name: 'custom',
   model: 'claude-sonnet-4-6',
-  toolPreset: 'readwrite',        // Start with: file_read, file_write, file_edit, grep
+  toolPreset: 'readwrite',        // Start with: file_read, file_write, file_edit, grep, glob
   tools: ['file_read', 'grep'],   // Allowlist: intersect with preset = file_read, grep
   disallowedTools: ['grep'],      // Denylist: subtract = file_read only
 }

src/agent/runner.ts

@@ -42,11 +42,13 @@ import type { ToolExecutor } from '../tool/executor.js'
 
 /** Predefined tool sets for common agent use cases. */
 export const TOOL_PRESETS = {
-  readonly: ['file_read', 'grep'],
+  readonly: ['file_read', 'grep', 'glob'],
-  readwrite: ['file_read', 'file_write', 'file_edit', 'grep'],
+  readwrite: ['file_read', 'file_write', 'file_edit', 'grep', 'glob'],
-  full: ['file_read', 'file_write', 'file_edit', 'grep', 'bash'],
+  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
@@ -213,6 +215,13 @@ export class AgentRunner {
    */
   private resolveTools(): LLMToolDef[] {
     // Validate configuration for contradictions
+    if (this.options.toolPreset && this.options.allowedTools) {
+      console.warn(
+        'AgentRunner: both toolPreset and allowedTools are set. ' +
+        'Final tool access will be the intersection of both.'
+      )
+    }
+
     if (this.options.allowedTools && this.options.disallowedTools) {
       const overlap = this.options.allowedTools.filter(tool =>
         this.options.disallowedTools!.includes(tool)
@@ -225,30 +234,33 @@ export class AgentRunner {
       }
     }
 
-    let tools = this.toolRegistry.toToolDefs()
+    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))
 
     // 1. Apply preset filter if set
     if (this.options.toolPreset) {
       const presetTools = new Set(TOOL_PRESETS[this.options.toolPreset] as readonly string[])
-      tools = tools.filter(t => presetTools.has(t.name))
+      builtInTools = builtInTools.filter(t => presetTools.has(t.name))
     }
 
     // 2. Apply allowlist filter if set
     if (this.options.allowedTools) {
-      tools = tools.filter(t => this.options.allowedTools!.includes(t.name))
+      builtInTools = builtInTools.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)
-      tools = tools.filter(t => !denied.has(t.name))
+      builtInTools = builtInTools.filter(t => !denied.has(t.name))
     }
 
     // 4. Apply framework-level safety rails
     const frameworkDenied = new Set(AGENT_FRAMEWORK_DISALLOWED)
-    tools = tools.filter(t => !frameworkDenied.has(t.name))
+    builtInTools = builtInTools.filter(t => !frameworkDenied.has(t.name))
 
-    return tools
+    // Custom tools stay available regardless of built-in filtering rules.
+    return [...builtInTools, ...customTools]
   }
 
   // -------------------------------------------------------------------------

tests/tool-filtering.test.ts

@@ -89,15 +89,15 @@ describe('Tool filtering', () => {
 
   describe('TOOL_PRESETS', () => {
     it('readonly preset has correct tools', () => {
-      expect(TOOL_PRESETS.readonly).toEqual(['file_read', 'grep'])
+      expect(TOOL_PRESETS.readonly).toEqual(['file_read', 'grep', 'glob'])
     })
 
     it('readwrite preset has correct tools', () => {
-      expect(TOOL_PRESETS.readwrite).toEqual(['file_read', 'file_write', 'file_edit', 'grep'])
+      expect(TOOL_PRESETS.readwrite).toEqual(['file_read', 'file_write', 'file_edit', 'grep', 'glob'])
     })
 
     it('full preset has correct tools', () => {
-      expect(TOOL_PRESETS.full).toEqual(['file_read', 'file_write', 'file_edit', 'grep', 'bash'])
+      expect(TOOL_PRESETS.full).toEqual(['file_read', 'file_write', 'file_edit', 'grep', 'glob', 'bash'])
     })
   })
 
@@ -124,7 +124,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['file_read', 'grep'])
+      expect(toolNames).toEqual(['custom_tool', 'file_read', 'grep'])
     })
 
     it('readwrite preset filters correctly', () => {
@@ -136,7 +136,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['file_edit', 'file_read', 'file_write', 'grep'])
+      expect(toolNames).toEqual(['custom_tool', 'file_edit', 'file_read', 'file_write', 'grep'])
     })
 
     it('full preset filters correctly', () => {
@@ -148,7 +148,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['bash', 'file_edit', 'file_read', 'file_write', 'grep'])
+      expect(toolNames).toEqual(['bash', 'custom_tool', 'file_edit', 'file_read', 'file_write', 'grep'])
     })
   })
 
@@ -162,7 +162,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['bash', 'file_read'])
+      expect(toolNames).toEqual(['bash', 'custom_tool', 'file_read'])
     })
 
     it('empty allowlist returns no tools', () => {
@@ -172,7 +172,7 @@ describe('Tool filtering', () => {
       })
 
       const tools = (runner as any).resolveTools()
-      expect(tools).toHaveLength(0)
+      expect((tools as LLMToolDef[]).map(t => t.name)).toEqual(['custom_tool'])
     })
   })
 
@@ -186,7 +186,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['file_edit', 'file_read', 'file_write', 'grep'])
+      expect(toolNames).toEqual(['custom_tool', 'file_edit', 'file_read', 'file_write', 'grep'])
     })
 
     it('empty denylist returns all tools', () => {
@@ -215,7 +215,7 @@ describe('Tool filtering', () => {
       const tools = (runner as any).resolveTools() as LLMToolDef[]
       const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
 
-      expect(toolNames).toEqual(['file_read', 'grep'])
+      expect(toolNames).toEqual(['custom_tool', 'file_read', 'grep'])
     })
 
     it('preset filters first, then allowlist intersects, then denylist subtracts', () => {
@@ -230,7 +230,23 @@ describe('Tool filtering', () => {
       })
 
       const tools = (runner as any).resolveTools()
-      expect(tools).toHaveLength(0)
+      expect((tools as LLMToolDef[]).map(t => t.name)).toEqual(['custom_tool'])
+    })
+  })
+
+  describe('resolveTools - custom tool behavior', () => {
+    it('always includes custom tools regardless of filtering', () => {
+      const runner = new AgentRunner(mockAdapter, registry, executor, {
+        model: 'test-model',
+        toolPreset: 'readonly',
+        allowedTools: ['file_read'],
+        disallowedTools: ['file_read', 'bash', 'grep'],
+      })
+
+      const tools = (runner as any).resolveTools() as LLMToolDef[]
+      const toolNames = tools.map((t: LLMToolDef) => t.name).sort()
+
+      expect(toolNames).toEqual(['custom_tool'])
     })
   })
 
@@ -259,6 +275,20 @@ describe('Tool filtering', () => {
       )
     })
 
+    it('warns when both toolPreset and allowedTools are set', () => {
+      const runner = new AgentRunner(mockAdapter, registry, executor, {
+        model: 'test-model',
+        toolPreset: 'readonly',
+        allowedTools: ['file_read', 'bash'],
+      })
+
+      ;(runner as any).resolveTools()
+
+      expect(consoleWarnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('both toolPreset and allowedTools are set')
+      )
+    })
+
     it('does not warn when no overlap between allowedTools and disallowedTools', () => {
       const runner = new AgentRunner(mockAdapter, registry, executor, {
         model: 'test-model',