refactor: reorganize into monorepo with separate subprojects

Structure webber into three independent subprojects:
- webber-api/: FastAPI backend server with all agent code
- webber-cli/: Standalone CLI client (renamed from cli/ to webber_cli/)
- webber-sandbox/: Test project for functional testing

Key changes:
- Each subproject has its own .venv (Python 3.12+)
- Added sandbox.sh for managing test project templates
- Created sandbox-templates/ with calculator-cli and empty starter
- Updated CI/CD for prefixed tags (api/v*, cli/v*)
- Added comprehensive AGENTS.md with operational instructions
- Added gitignore filtering to glob and grep tools
- Created pyproject.toml for each subproject

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

webber-api/src/domains/agents/explore/agent.py

@@ -0,0 +1,127 @@
+"""
+Explore Agent implementation using PydanticAI.
+
+Fast codebase exploration with read-only tools.
+Uses sanitized Ollama provider for reliable tool calling.
+"""
+import os
+from dataclasses import dataclass
+from typing import Any
+
+from pydantic_ai import Agent
+from pydantic_ai.models.openai import OpenAIModel
+
+from src.domains.agents.base import BaseAgent, AgentContext, register_agent
+from src.domains.agents.explore.prompts import EXPLORE_SYSTEM_PROMPT
+from src.ollama.provider import get_ollama_provider
+from src.shared.config import get_settings
+from src.shared.logging import logged, get_logger, trace_span
+
+logger = get_logger(__name__)
+
+
+@dataclass
+class ExploreContext(AgentContext):
+    """
+    Context for explore agent tools.
+
+    Passed to all tool functions via RunContext.
+    """
+    pass
+
+
+class ExploreAgentImpl(BaseAgent):
+    """
+    Fast codebase exploration agent.
+
+    Uses glob, grep, read, and bash tools to search and analyze codebases.
+    Read-only mode - cannot modify files.
+    """
+
+    name = "explore"
+    description = "Fast codebase exploration - find files, search content, read code"
+
+    def __init__(self):
+        """Initialize the explore agent."""
+        self._agent: Agent[ExploreContext, str] | None = None
+        self._settings = get_settings()
+
+    def _create_agent(self) -> Agent[ExploreContext, str]:
+        """Create the PydanticAI agent with Ollama backend."""
+        # Use sanitized Ollama provider to fix content: null issues
+        model = OpenAIModel(
+            model_name=self._settings.ollama_agent_model,
+            provider=get_ollama_provider(),
+        )
+
+        agent: Agent[ExploreContext, str] = Agent(
+            model=model,
+            system_prompt=EXPLORE_SYSTEM_PROMPT,
+            deps_type=ExploreContext,
+            output_type=str,
+            # Mistral Nemo settings:
+            # - temperature 0.3 (Nemo needs slightly higher than 0.0)
+            # - tool_choice "required" forces tool use
+            model_settings={
+                "temperature": 0.3,
+                "extra_body": {"tool_choice": "required"},
+            },
+        )
+
+        # Register tools
+        self._register_tools(agent)
+
+        return agent
+
+    def _register_tools(self, agent: Agent[ExploreContext, str]) -> None:
+        """Register all exploration tools with the agent."""
+        from src.domains.agents.explore.tools import register_explore_tools
+        register_explore_tools(agent)
+
+    @logged()
+    async def run(
+        self,
+        prompt: str,
+        working_dir: str | None = None,
+        allowed_paths: list[str] | None = None,
+        **kwargs: Any
+    ) -> str:
+        """
+        Run the explore agent with a prompt.
+
+        Args:
+            prompt: User query about the codebase
+            working_dir: Working directory for exploration
+            allowed_paths: Restrict tool access to these paths
+
+        Returns:
+            Agent response with findings
+        """
+        ctx = ExploreContext(
+            working_dir=working_dir or os.getcwd(),
+            allowed_paths=allowed_paths or self._settings.effective_allowed_paths,
+            timeout_seconds=self._settings.tool_timeout_seconds,
+        )
+
+        async with trace_span("explore_agent_run"):
+            try:
+                # Use run() not run_stream() - Ollama has bugs with streaming + tools
+                result = await self.agent.run(prompt, deps=ctx)
+                return result.output
+            except Exception as e:
+                logger.exception(f"Explore agent error: {e}")
+                raise
+
+
+# Create and register the singleton instance
+explore_agent = ExploreAgentImpl()
+register_agent(explore_agent)
+
+
+async def explore(
+    prompt: str,
+    working_dir: str | None = None,
+    **kwargs: Any
+) -> str:
+    """Run exploration query."""
+    return await explore_agent.run(prompt, working_dir=working_dir, **kwargs)