For example using gcc -MM does not work with subfolders, a depend rule requires the user to use it everytimes he adds new files ...

Here is what is wanted:

• Completly automatic: No user interaction is required when adding new files
• Works with an arbitrary amount of files
• Works with an arbitrary amount of level of folders
• Is not recalculated when nothing changed
• Use only one file to store dependencies
• Do not depend on complicated regular expressions

Here is the result:

BINARY  = project.exe
CC      = gcc
CFLAGS  = 
FILES   = $(shell find src/ -name "*.c")
HEADERS = $(shell find src/ -name "*.h")
OBJS    = $(FILES:.c=.o)
 
all: $(BINARY)
 
-include Makefile.deps
 
$(BINARY): Makefile.deps $(OBJS)
        $(CC) $(CFLAGS) $(OBJS) -o $(BINARY)
 
Makefile.deps: $(FILES) $(HEADERS)
        makedepend -- $(CFLAGS) -- $(FILES) -f- > Makefile.deps

This is in fact really easy. In your $(BINARY) rule, you add Makefile.deps as a prerequisite.

In order to generate the Makefile.deps you mark all $(FILES) and $(HEADERS) as prerequisite, so every time you change a file or header it will recompile the list.
We use makedepend to generate the dependencies list. It works like gcc -MM except that it outputs the correct file path when used with folders.

Then all is required is to include the Makefile.deps. We include it with -include so it does work the first time you compile.

Thanks to Lemoine Gauthier who helped me to discover this technique.