feat(plugins): Stage 2.1 — plugin framework and AI tool-use

Introduces a standalone plugin system where every integration lives as
an independent Python script in ~/.pyra/plugins/, not hardcoded in core.

Plugin framework (src/pyra/plugins/):
- base.py: Tool dataclass, PyraPlugin Protocol, BasePlugin helper
- loader.py: importlib-based discovery; one bad plugin never crashes pyra
- registry.py: singleton aggregating tools, slash commands, system prompts
- executor.py: approval gate — scans args, prompts y/N, scans result, logs
- install.py: copies bundled_plugins/ to ~/.pyra/plugins/ on install

Chat integration:
- AI tool-use loop (litellm function calling, up to 10 iterations)
- Plugin system prompt additions injected per session
- Plugin slash commands merged with static commands

CLI additions:
- pyra plugin list/install/enable/disable/setup
- pyra daemon start/stop/status/restart/install/uninstall (stubs for 2.4)

Config: PluginConfig + DaemonConfig added to PyraConfig (backwards-compatible)
Bootstrap: ~/.pyra/plugins/ and ~/.pyra/logs/ created on startup
Security: tool args and results always injection-scanned; plugin dirs
validated with assert_safe_path() before loading (symlink protection)

Tests: 37 new tests (loader, registry, executor, plugin isolation security)
161 total, all passing.

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

src/pyra/plugins/registry.py

@@ -0,0 +1,84 @@
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Callable, Coroutine
+
+from pyra.plugins.base import PyraPlugin, Tool
+from pyra.plugins.loader import _log_error, load_plugins
+from pyra.vault.reader import get_key
+
+
+class PluginRegistry:
+    _instance: PluginRegistry | None = None
+
+    def __init__(self) -> None:
+        self._plugins: dict[str, PyraPlugin] = {}
+
+    @classmethod
+    def instance(cls) -> PluginRegistry:
+        if cls._instance is None:
+            cls._instance = cls()
+        return cls._instance
+
+    @classmethod
+    def reset(cls) -> None:
+        """Reset singleton — for tests only."""
+        cls._instance = None
+
+    def load_all(self, plugins_dir: Path, enabled_names: list[str]) -> None:
+        all_plugins = load_plugins(plugins_dir)
+        self._plugins = {}
+        for plugin in all_plugins:
+            if plugin.name in enabled_names:
+                try:
+                    plugin.on_load(get_key)
+                    self._plugins[plugin.name] = plugin
+                except Exception as exc:
+                    _log_error(plugin.name, exc)
+
+    def get_active_plugins(self) -> list[PyraPlugin]:
+        return list(self._plugins.values())
+
+    def get_all_tools(self) -> list[Tool]:
+        tools: list[Tool] = []
+        for plugin in self._plugins.values():
+            try:
+                tools.extend(plugin.tools())
+            except Exception:
+                pass
+        return tools
+
+    def get_slash_commands(self) -> dict[str, Callable[[], None]]:
+        cmds: dict[str, Callable[[], None]] = {}
+        for plugin in self._plugins.values():
+            try:
+                cmds.update(plugin.slash_commands())
+            except Exception:
+                pass
+        return cmds
+
+    def get_system_prompt_additions(self) -> str:
+        parts: list[str] = []
+        for plugin in self._plugins.values():
+            try:
+                addition = plugin.system_prompt_addition()
+                if addition:
+                    parts.append(addition.strip())
+            except Exception:
+                pass
+        return "\n\n".join(parts)
+
+    def get_daemon_tasks(self) -> list[Coroutine]:  # type: ignore[type-arg]
+        tasks: list[Coroutine] = []  # type: ignore[type-arg]
+        for plugin in self._plugins.values():
+            try:
+                tasks.extend(plugin.daemon_tasks())
+            except Exception:
+                pass
+        return tasks
+
+    def find_tool(self, name: str) -> Tool | None:
+        for tool in self.get_all_tools():
+            if tool.name == name:
+                return tool
+        return None