Add Phase 6: write tools, shell, and edit tools with reasoning-only fix

Implement 6 new agent tools — write_file, make_dir, delete_file,
str_replace, patch_apply, run_command — bringing the agent from
read-only observer to active code modifier. All write/shell operations
are gated through the existing permissions service.

Also fix a bug where qwen3.5 thinking mode produces reasoning tokens
but no content after tool results, causing the agent to silently exit.
The loop now detects reasoning-only responses, retries twice, then
injects a nudge message to break the model out of its thinking loop.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app/tools/filesystem.py

@@ -1,4 +1,4 @@
-"""Filesystem tools: read_file and list_dir."""
+"""Filesystem tools: read_file, list_dir, write_file, make_dir, delete_file."""
 
 from pathlib import Path
 from typing import Any
@@ -13,6 +13,7 @@ from app.utils.file_helpers import (
     PathSecurityError,
     resolve_safe_path,
     safe_read_file,
+    safe_write_file,
 )
 
 
@@ -147,3 +148,175 @@ class ListDirTool(BaseTool):
             status=ToolResultStatus.SUCCESS,
             output="\n".join(lines),
         )
+
+
+class WriteFileParams(BaseModel):
+    """Parameters for the write_file tool."""
+
+    file_path: str = Field(description="Path to the file to write (relative to workspace root)")
+    content: str = Field(description="Content to write to the file")
+
+
+class WriteFileTool(BaseTool):
+    """Write content to a file within the workspace."""
+
+    name = "write_file"
+    description = (
+        "Write text content to a file. Creates parent directories if needed. "
+        "Overwrites existing file content."
+    )
+    params_model = WriteFileParams
+
+    def execute(self, *, tool_call_id: str, file_path: str, content: str, **kwargs: Any) -> ToolResult:
+        fs_config = self.config.tools.filesystem
+        try:
+            safe_path = safe_write_file(
+                file_path,
+                content,
+                self.workspace_root,
+                max_size_bytes=fs_config.max_file_size_bytes,
+            )
+        except PathSecurityError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=str(exc),
+            )
+        except FileSizeError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=str(exc),
+            )
+
+        try:
+            rel_path = safe_path.relative_to(self.workspace_root)
+        except ValueError:
+            rel_path = safe_path
+
+        return ToolResult(
+            tool_call_id=tool_call_id,
+            tool_name=self.name,
+            status=ToolResultStatus.SUCCESS,
+            output=f"Wrote {len(content)} characters to {rel_path}",
+        )
+
+
+class MakeDirParams(BaseModel):
+    """Parameters for the make_dir tool."""
+
+    directory_path: str = Field(description="Path to the directory to create (relative to workspace root)")
+
+
+class MakeDirTool(BaseTool):
+    """Create a directory (and any missing parents) within the workspace."""
+
+    name = "make_dir"
+    description = "Create a directory and any necessary parent directories."
+    params_model = MakeDirParams
+
+    def execute(self, *, tool_call_id: str, directory_path: str, **kwargs: Any) -> ToolResult:
+        try:
+            safe_path = resolve_safe_path(directory_path, self.workspace_root)
+        except PathSecurityError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=str(exc),
+            )
+
+        if safe_path.exists() and not safe_path.is_dir():
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=f"Path exists and is not a directory: {safe_path}",
+            )
+
+        try:
+            safe_path.mkdir(parents=True, exist_ok=True)
+        except OSError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=f"Failed to create directory: {exc}",
+            )
+
+        try:
+            rel_path = safe_path.relative_to(self.workspace_root)
+        except ValueError:
+            rel_path = safe_path
+
+        return ToolResult(
+            tool_call_id=tool_call_id,
+            tool_name=self.name,
+            status=ToolResultStatus.SUCCESS,
+            output=f"Created directory: {rel_path}",
+        )
+
+
+class DeleteFileParams(BaseModel):
+    """Parameters for the delete_file tool."""
+
+    file_path: str = Field(description="Path to the file to delete (relative to workspace root)")
+
+
+class DeleteFileTool(BaseTool):
+    """Delete a file within the workspace. Refuses to delete directories."""
+
+    name = "delete_file"
+    description = "Delete a single file. Does not delete directories."
+    params_model = DeleteFileParams
+
+    def execute(self, *, tool_call_id: str, file_path: str, **kwargs: Any) -> ToolResult:
+        try:
+            safe_path = resolve_safe_path(file_path, self.workspace_root)
+        except PathSecurityError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=str(exc),
+            )
+
+        if safe_path.is_dir():
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=f"Path is a directory, not a file: {safe_path}",
+            )
+
+        if not safe_path.exists():
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=f"File not found: {safe_path}",
+            )
+
+        try:
+            safe_path.unlink()
+        except OSError as exc:
+            return ToolResult(
+                tool_call_id=tool_call_id,
+                tool_name=self.name,
+                status=ToolResultStatus.ERROR,
+                error=f"Failed to delete file: {exc}",
+            )
+
+        try:
+            rel_path = safe_path.relative_to(self.workspace_root)
+        except ValueError:
+            rel_path = safe_path
+
+        return ToolResult(
+            tool_call_id=tool_call_id,
+            tool_name=self.name,
+            status=ToolResultStatus.SUCCESS,
+            output=f"Deleted: {rel_path}",
+        )