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/tools.py

@@ -0,0 +1,163 @@
+"""
+Tool registrations for the Explore agent.
+
+Registers our tool implementations with the PydanticAI agent.
+"""
+from pydantic_ai import Agent, RunContext
+
+from src.domains.agents.base import AgentContext
+from src.domains.tools.file.read import ReadFileTool
+from src.domains.tools.file.glob import GlobFilesTool
+from src.domains.tools.search.grep import GrepContentTool
+from src.domains.tools.shell.bash import BashReadOnlyTool
+
+
+def register_explore_tools(agent: Agent[AgentContext, str]) -> None:
+    """
+    Register all exploration tools with the agent.
+
+    Each tool is wrapped to use context from RunContext.
+    """
+
+    @agent.tool
+    async def read_file(
+        ctx: RunContext[AgentContext],
+        file_path: str,
+        offset: int = 0,
+        limit: int = 2000
+    ) -> str:
+        """Read contents of a file with line numbers.
+
+        Args:
+            file_path: Absolute path to the file to read
+            offset: Line number to start from (0-based, default: 0)
+            limit: Maximum number of lines to read (default: 2000)
+
+        Returns:
+            File contents with line numbers, or error message.
+
+        IMPORTANT: Always use absolute paths. Never guess file contents.
+        """
+        tool = ReadFileTool(allowed_paths=ctx.deps.allowed_paths)
+        result = await tool.execute(
+            file_path=file_path,
+            offset=offset,
+            limit=limit
+        )
+        return result.to_string()
+
+    @agent.tool
+    async def glob_files(
+        ctx: RunContext[AgentContext],
+        pattern: str,
+        path: str | None = None,
+        limit: int = 100
+    ) -> str:
+        """Find files matching a glob pattern.
+
+        Args:
+            pattern: Glob pattern (e.g., "**/*.py", "src/**/*.ts", "*.md")
+            path: Directory to search in (default: working directory)
+            limit: Maximum number of files to return (default: 100)
+
+        Returns:
+            List of absolute file paths, sorted by modification time (newest first).
+
+        Examples:
+            - "**/*.py" finds all Python files
+            - "src/**/*.ts" finds TypeScript files in src/
+            - "**/test_*.py" finds all test files
+
+        IMPORTANT: Use this to discover files before reading them.
+        """
+        tool = GlobFilesTool(allowed_paths=ctx.deps.allowed_paths)
+        search_path = path or ctx.deps.working_dir
+        result = await tool.execute(
+            pattern=pattern,
+            path=search_path,
+            limit=limit
+        )
+        return result.to_string()
+
+    @agent.tool
+    async def grep_content(
+        ctx: RunContext[AgentContext],
+        pattern: str,
+        path: str | None = None,
+        file_glob: str | None = None,
+        context_lines: int = 0,
+        case_sensitive: bool = True
+    ) -> str:
+        """Search file contents using regex pattern.
+
+        Args:
+            pattern: Regex pattern to search for (Python re syntax)
+            path: Directory or file to search (default: working directory)
+            file_glob: Filter files by glob (e.g., "*.py", "*.ts")
+            context_lines: Lines of context before/after matches (default: 0)
+            case_sensitive: Case-sensitive search (default: True)
+
+        Returns:
+            Matching lines with file paths and line numbers.
+            Format: "filepath:line_num: content"
+
+        Examples:
+            - pattern="def.*__init__" finds init methods
+            - pattern="class\\s+\\w+" finds class definitions
+            - pattern="TODO|FIXME" finds todo comments
+
+        IMPORTANT: Use this to search for code patterns. Escape regex special chars.
+        """
+        tool = GrepContentTool(allowed_paths=ctx.deps.allowed_paths)
+        search_path = path or ctx.deps.working_dir
+        result = await tool.execute(
+            pattern=pattern,
+            path=search_path,
+            file_glob=file_glob,
+            context_lines=context_lines,
+            case_sensitive=case_sensitive
+        )
+        return result.to_string()
+
+    @agent.tool
+    async def bash_readonly(
+        ctx: RunContext[AgentContext],
+        command: str,
+        cwd: str | None = None,
+        timeout: int = 30
+    ) -> str:
+        """Execute a read-only bash command.
+
+        ALLOWED commands:
+        - File inspection: ls, find, cat, head, tail, wc, file, stat, tree, du
+        - Git (read-only): git status, git log, git diff, git show, git branch
+        - Text processing: grep, awk, sed (read-only), sort, uniq
+        - System info: pwd, whoami, hostname, which
+
+        FORBIDDEN:
+        - File modification (rm, mv, cp, mkdir, touch)
+        - Redirects (>, >>)
+        - Command chaining (&&, ||, ;)
+        - Network (curl, wget)
+
+        Args:
+            command: The bash command to execute
+            cwd: Working directory (default: agent working directory)
+            timeout: Timeout in seconds (default: 30)
+
+        Returns:
+            Command output or error message.
+
+        Examples:
+            - "ls -la" lists files with details
+            - "git status" shows git status
+            - "git log --oneline -10" shows recent commits
+        """
+        tool = BashReadOnlyTool(allowed_paths=ctx.deps.allowed_paths)
+        working_dir = cwd or ctx.deps.working_dir
+        result = await tool.execute(
+            command=command,
+            cwd=working_dir,
+            timeout=min(timeout, ctx.deps.timeout_seconds)
+        )
+        return result.to_string()