feat: add agent subagent support, bash timeout, context manager improvements, and benchmark script

- Add agent_set_is_subagent and agent_set_tool_registry to agent API for subagent support
- Add timeout_seconds parameter to r_bash_execute to prevent hanging processes
- Refactor context_manager truncation logic with dynamic ratio-based truncation and total size calculation
- Add messages_to_json_string helper and r_config_get_max_tokens accessor
- Introduce tool_registry_get_specialized for type-filtered tool registries
- Add completion_phrases and passive_phrases detection to agent completion logic
- Suppress spinner in http_client when stderr is not a TTY
- Add comprehensive agent_benchmark.py with TestCase framework and logging

include/agent.h

@@ -5,6 +5,7 @@
 
 #include "messages.h"
 #include "r_error.h"
+#include "tool.h"
 #include <stdbool.h>
 
 #define AGENT_MAX_ITERATIONS 300
@@ -26,6 +27,8 @@ void agent_destroy(agent_handle agent);
 
 void agent_set_max_iterations(agent_handle agent, int max);
 void agent_set_verbose(agent_handle agent, bool verbose);
+void agent_set_is_subagent(agent_handle agent, bool is_subagent);
+void agent_set_tool_registry(agent_handle agent, tool_registry_t *registry);
 
 agent_state_t agent_get_state(agent_handle agent);
 const char *agent_get_error(agent_handle agent);

include/bash_executor.h

@@ -4,6 +4,6 @@
 
 #include <stdbool.h>
 
-char *r_bash_execute(const char *command, bool interactive);
+char *r_bash_execute(const char *command, bool interactive, int timeout_seconds);
 
 #endif

include/messages.h

@@ -32,6 +32,7 @@ r_status_t messages_replace_at(messages_handle msgs, int index, struct json_obje
 
 struct json_object *messages_to_json(messages_handle msgs);
 char *messages_to_string(messages_handle msgs);
+char *messages_to_json_string(messages_handle msgs);
 int messages_count(messages_handle msgs);
 
 #endif

include/r_config.h

@@ -24,6 +24,7 @@ bool r_config_is_verbose(r_config_handle cfg);
 void r_config_set_verbose(r_config_handle cfg, bool verbose);
 
 double r_config_get_temperature(r_config_handle cfg);
+int r_config_get_max_tokens(r_config_handle cfg);
 
 const char *r_config_get_session_id(r_config_handle cfg);
 bool r_config_set_session_id(r_config_handle cfg, const char *session_id);

include/tool.h

@@ -39,4 +39,13 @@ struct json_object *tool_registry_execute(tool_registry_t *registry,
 tool_registry_t *tools_get_registry(void);
 void tools_registry_shutdown(void);
 
+typedef enum {
+    TOOL_TYPE_ALL,
+    TOOL_TYPE_RESEARCHER,
+    TOOL_TYPE_DEVELOPER,
+    TOOL_TYPE_SECURITY
+} tool_registry_type_t;
+
+tool_registry_t *tool_registry_get_specialized(tool_registry_type_t type);
+
 #endif