Update.

Makefile

@@ -1,75 +1,94 @@
-all: build build_rpylib run build_mingw
+# retoor <retoor@molodetz.nl>
 
-# Variables for compiler and flags
 CC = gcc
-CFLAGS = -Ofast -Werror -Wall  -lreadline -lncurses  -lcurl -ljson-c -lsqlite3 -lm -lpthread $(pkg-config --cflags --libs gnutls gmp) -lssl -lcrypto 
+CFLAGS = -Ofast -Werror -Wall -I./include
+LDFLAGS = -lreadline -lncurses -lcurl -ljson-c -lsqlite3 -lm -lpthread -lssl -lcrypto
 
-# MinGW Variables
-MINGW_CC = x86_64-w64-mingw32-gcc  # Change to x86_64-w64-mingw32-gcc for 64-bit
-MINGW_CFLAGS = -Ofast -Werror -Wall -lreadline -lcurl -lssl -lcrypto -ljson-c -lm -lglob
+SRCDIR = src
+TOOLSDIR = src/tools
+BUILDDIR = build
+BINDIR = bin
 
-# Targets
-build: publish 
-	mkdir -p bin
-	$(CC) main.c $(CFLAGS) -o bin/r 
-	cp bin/r r
-	publish r
+SRC_CORE = $(SRCDIR)/r_error.c \
+           $(SRCDIR)/r_config.c \
+           $(SRCDIR)/tool_registry.c \
+           $(SRCDIR)/db.c \
+           $(SRCDIR)/http_client.c \
+           $(SRCDIR)/messages.c \
+           $(SRCDIR)/agent.c \
+           $(SRCDIR)/bash_executor.c \
+           $(SRCDIR)/main.c
 
-appimage:
-	-@rm -rf AppImage	
-	mkdir -p AppImage
-	mkdir -p AppImage/usr 
-	mkdir -p AppImage/usr/bin
-	mkdir -p AppImage/lib 
-	cp AppRun AppImage/AppRun
-	cp r.desktop AppImage/r.desktop 
-	cp r.png AppImage/r.png 
-	cp bin/r AppImage/usr/bin/r	
-	./collect_so_files.sh
-	#./prepare_app_image AppImage/usr/bin/r AppImage	
-	appimagetool-x86_64.AppImage AppImage
-	mv r-x86_64.AppImage r
+SRC_TOOLS = $(TOOLSDIR)/tools_init.c \
+            $(TOOLSDIR)/tool_terminal.c \
+            $(TOOLSDIR)/tool_file.c \
+            $(TOOLSDIR)/tool_db.c \
+            $(TOOLSDIR)/tool_http.c \
+            $(TOOLSDIR)/tool_python.c \
+            $(TOOLSDIR)/tool_indexer.c
 
-publish:
-	curl -OJ https://retoor.molodetz.nl/api/packages/retoor/generic/publish/1.0.0/publish
-	chmod +x publish 
-	./publish r
+SRC = $(SRC_CORE) $(SRC_TOOLS)
 
+OBJ_CORE = $(patsubst $(SRCDIR)/%.c,$(BUILDDIR)/%.o,$(SRC_CORE))
+OBJ_TOOLS = $(patsubst $(TOOLSDIR)/%.c,$(BUILDDIR)/tools/%.o,$(SRC_TOOLS))
+OBJ = $(OBJ_CORE) $(OBJ_TOOLS)
+
+.PHONY: all clean build build_legacy run
+
+all: build
+
+build: $(BINDIR)/r
+	cp $(BINDIR)/r r
+
+$(BINDIR)/r: $(OBJ)
+	@mkdir -p $(BINDIR)
+	$(CC) $(OBJ) $(LDFLAGS) -o $@
+
+$(BUILDDIR)/%.o: $(SRCDIR)/%.c
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -c $< -o $@
+
+$(BUILDDIR)/tools/%.o: $(TOOLSDIR)/%.c
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -c $< -o $@
+
+build_legacy:
+	@mkdir -p $(BINDIR)
+	$(CC) main.c $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/r_legacy
+	cp $(BINDIR)/r_legacy r
 
 build_rpylib:
 	$(CC) -shared -o rpylib.so -fPIC rpylib.c -lpython3.12 `python3-config --includes` -I/usr/include/CL -ljson-c -lcurl -lsqlite3
-	publish rpylib.so
 
-# New MinGW build target
-build_mingw:
-	$(MINGW_CC) main.c $(MINGW_CFLAGS) -o r.exe
-	publish r.exe
-
-run: 
+run: build
 	./r --verbose
 
-run_free:
-	./rf --verbose 
+install:
+	cp ./r /usr/local/bin/r
 
-run_rd:
-	./rd --verbose 
-
-run_mingw:
-	./r.exe --verbose
+clean:
+	rm -rf $(BUILDDIR) $(BINDIR)
+	rm -f r
 
+appimage: build
+	-@rm -rf AppImage
+	mkdir -p AppImage/usr/bin
+	mkdir -p AppImage/lib
+	cp AppRun AppImage/AppRun
+	cp r.desktop AppImage/r.desktop
+	cp r.png AppImage/r.png
+	cp $(BINDIR)/r AppImage/usr/bin/r
+	./collect_so_files.sh
+	appimagetool-x86_64.AppImage AppImage
+	mv r-x86_64.AppImage r
 
 docker: docker_make docker_run
+
 docker_make:
 	docker build -t r .
+
 docker_run:
 	docker run -v .:/app --rm -it r
 
 build_deb:
 	dpkg-deb --build r_package
-
-# --- RAG Side Project ---
-rag_test: rag_test.c rag.c db_utils.c rag.h db_utils.h
-	$(CC) -o rag_test rag_test.c rag.c db_utils.c -lsqlite3 -ljson-c
-
-run_rag_test: rag_test
-	./rag_test