From 4c37aa83dfa7890aca1ba604a01199b041fa6feb Mon Sep 17 00:00:00 2001
From: Gilles Ceyssat <gilles.ceyssat@gmail.com>
Date: Tue, 12 May 2026 07:53:56 +0400
Subject: [PATCH] feat(executor): pull SystemBuilder MCP tools into agent's
 tool list
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The AgentExecutor builds agents from a template's `tools` whitelist by
resolving each name against the static `ToolRegistry`. External MCP
tools (discovered at SystemBuilder.build() time via _discover_external_mcp)
were never picked up — they exist on system.tool_executor._tools but
the per-agent build path never read from there.

Result: any agent whose template declared MCP tool names by name got
0 of them at runtime, falling back to natives only. The agent's system
prompt could still mention the tools, but the model could not call them
(only shell_exec or other native fallbacks were available).

This adds a fallback after the ToolRegistry loop: for any tool name not
resolved from the registry, look it up in system.tool_executor._tools
and append the already-instantiated MCP adapter. Native tools still
take precedence (same name, the registry hit wins).

Verified by configuring a CyberStrikeAI stdio MCP server (78 tools).
Before this patch: agent built with 4 tools. After: 4 native + 78 MCP.
---
 src/openjarvis/agents/executor.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/openjarvis/agents/executor.py b/src/openjarvis/agents/executor.py
index 8d6be76f..cc60c6a7 100644
--- a/src/openjarvis/agents/executor.py
+++ b/src/openjarvis/agents/executor.py
@@ -317,6 +317,21 @@ class AgentExecutor:
                         tool_instances.append(tool)
                     except Exception:
                         logger.warning("Failed to instantiate tool %s", tname)
+
+            # Pull tools already discovered by SystemBuilder (e.g. external MCP
+            # adapters) that aren't in the static ToolRegistry. Without this,
+            # agents declaring MCP-discovered tools in their template would
+            # silently fall back to natives only.
+            if self._system is not None and getattr(self._system, "tool_executor", None) is not None:
+                mcp_pool = getattr(self._system.tool_executor, "_tools", {}) or {}
+                existing = {t.spec.name for t in tool_instances}
+                for tname in tool_names:
+                    if tname in existing:
+                        continue
+                    pooled = mcp_pool.get(tname)
+                    if pooled is not None:
+                        tool_instances.append(pooled)
+
             if tool_instances:
                 logger.info(
                     "Agent %s: resolved %d/%d tools",
@@ -332,6 +347,12 @@ class AgentExecutor:
             agent_kwargs["system_prompt"] = sys_prompt
         if getattr(agent_cls, "accepts_tools", False) and tool_instances:
             agent_kwargs["tools"] = tool_instances
+        # Propagate confirmation policy from the AgentExecutor down to the
+        # agent's own ToolExecutor. Set by CLI paths like `jarvis agents ask`
+        # so non-interactive runs can auto-approve tool execution.
+        if getattr(self, "_confirm_callback", None) is not None:
+            agent_kwargs["interactive"] = True
+            agent_kwargs["confirm_callback"] = self._confirm_callback
         try:
             agent_instance = agent_cls(engine, model, **agent_kwargs)
         except TypeError: