feat: add bash_repair, context_manager, json_repair, python_repair, and r_diff modules with Makefile integration

Makefile

@@ -18,6 +18,7 @@ SRC_CORE = $(SRCDIR)/r_error.c \
            $(SRCDIR)/agent.c \
            $(SRCDIR)/bash_executor.c \
            $(SRCDIR)/context_manager.c \
+           $(SRCDIR)/r_diff.c \
            $(SRCDIR)/main.c
 
 SRC_TOOLS = $(TOOLSDIR)/tools_init.c \
@@ -26,7 +27,14 @@ SRC_TOOLS = $(TOOLSDIR)/tools_init.c \
             $(TOOLSDIR)/tool_db.c \
             $(TOOLSDIR)/tool_http.c \
             $(TOOLSDIR)/tool_python.c \
-            $(TOOLSDIR)/tool_indexer.c
+            $(TOOLSDIR)/tool_indexer.c \
+            $(TOOLSDIR)/tool_code.c \
+            $(TOOLSDIR)/tool_file_edit.c \
+            $(TOOLSDIR)/tool_system.c \
+            $(TOOLSDIR)/tool_network.c \
+            $(TOOLSDIR)/tool_dns.c \
+            $(TOOLSDIR)/tool_automation.c \
+            $(TOOLSDIR)/tool_csv.c
 
 SRC = $(SRC_CORE) $(SRC_TOOLS)