After working with Arduino for some years now there is one thing that still bothers me:
The way I work requires to have some more things in a sketch directory than just the .ino, .h and .cpp files. I often use a Makefile (to make printing more comfortable) or I put schematics, datasheets and such stuff there. And my way of working is to save quite often under different names - e. g. I save the sketch "lampe" as "lampe_0_9" where 0_9 means that its version is 0.9
Unfortunately non-Arduino files don't "move" to the new directory, I alwas have to search/copy them.
Maybe this can be fixed by adding a "save as mode" option to the preferences - something like "save as just copies Arduino files" vs. "save as recursively copies whole directory" ...?
It sounds like you have outgrown the IDE. Perhaps something a little more professional like Eclipse would be better for you.
It also sounds like you need to get on the boat about version control. You can decide that the standard methods aren't for you and you want to do your own thing, but you can't complain to others when your own thing doesn't work very well. It's like deciding you want to drive on the other side of the road and then getting mad because all these people are in your way. I know git sounds difficult when you first read about it, but IDEs like Eclipse have tools to help integrate it pretty painlessly.
If you put the extra files in the data subfolder of your sketch they will be copied along with the source files when you save as.
Although I don't take this as evidence that you've outgrown the Arduino IDE, I do strongly recommend that you start to use Git. It's not something to inflict on a beginner in their first month of programming but clearly you're far beyond that stage.
I don't see any benefit to an IDE with Git integration. Instead, I would find a dedicated Git client program that you like (unless you're happy with using Git from the command line exclusively, then don't bother). That will be much more flexible than hoping to find an IDE that happens to provide the development features you want as well as the version control features you want. I started with GitHub Desktop (which works for local repositories as well as repositories hosted on GitHub). At that time, it was a very nice beginner-friendly program, but limited in features. I know they've done a lot of development on it since I quit using it so I can't vouch for the program in its current form, but I suspect it's still good. I'm now using Git Extensions, which is excellent but unfortunately currently Windows-only.
Yes, it seems I've outgrown the Arduino IDE. The points are that I like to work with the "most original" and "most low-level" tools - and I don't want to use a service that requires me to be online (at least when checking in/out).
Anyway, putting "Makefile" in a "sketch/data" subdirectory works fine. If things get more complex I'll learn how to use cvs or something like that locally.
and I don't want to use a service that requires me to be online (at least when checking in/out).
If you mean git it doesn’t require that. It runs completely on your local machine. GitHub is just a place to share repos, but it isn’t required in any way.