I really hate the way Ableton handles file management!

[mekanism1200]

Yeah I don't think renaming the source files (even as an option) is a good idea at all. The OP is complaining about having files not save with a project to start with. Imagin if you had the option in Prefs (that you forgot you selected) then start renaming clips in a project and having that break reference to all your other tracks. No thanks.

I think the OP has now figured out and Stromkraft has explained it in detail (to summarise):
When you wish to make a completely self contained project from a template you need to first do a "Save AS" then save the project to a completely new folder (not within the template folder or it will simply create a new ALS file within the same project folder) Then a "Collect All and Save" once the project is in it's own folder.

Once you know how it works it does make sense and isn't an issue. I don't believe saving all your samples together in a new project folder on Save AS for a new project is a good idea since most people will have a well maintained library they are happy to read their samples from instead of having hundreds of copies taking up space.

A couple of tips though learned over the years from similar situations, if you are relying on this kind of stuff to make a living:
- Maintain backups... constant, incremental and automated if possible. I have a server that backups my machine automatically every hour and when it is first switched on to incremental packages. I can go back in time about 2 years to any point to find files even if they were deleted. Has saved me a few times!
- If you have to delete content from your HDD try and move it to a temp folder first and leave it there for a few weeks OR first empty your recycle bin then delete everything you need but don't empty the bin until you HAVE to. That will keep your samples in case you need them again.

Yeah you make some good points. Now that I know things work this way I wont make the same mistake again. I already plan on getting an NAS so backing up projects will be easier. My HDD is 4 years old now anyway so I dont want to rely on it for much longer.