Install each program in a dedicated directory tree, and use Stow or XStow to make all the programs appear in a common hierarchy. Stow creates symbolic links from the program-specific directory to a common tree.
In more detail, pick a toplevel directory, for example
/usr/local/stow. Install each program under
/usr/local/stow/PROGRAM_NAME. For example, arrange for its executables to be installed in
/usr/local/stow/PROGRAM_NAME/bin, its man pages in
/usr/local/stow/man/man1 and so on. If the program uses autoconf, then run
./configure --prefix /usr/local/stow/PROGRAM_NAME. After you've run
make install, run
./configure --prefix /usr/local/stow/PROGRAM_NAME
sudo make install
sudo stow PROGRAM_NAME
And now you'll have symbolic links like these:
/usr/local/bin/foo -> ../stow/PROGRAM_NAME/bin/foo
/usr/local/man/man1/foo.1 -> ../../stow/PROGRAM_NAME/man/man1/foo.1
/usr/local/lib/foo -> ../stow/PROGRAM_NAME/lib/foo
You can easily keep track of what programs you have installed by listing the contents of the
stow directory, and you always know what program a file belongs to because it's a symbolic link to a location under that program's directory. Uninstall a program by running
stow -D PROGRAM_NAME then deleting the program's directory. You can make a program temporarily unavailable by running
stow -D PROGRAM_NAME (run
stow PROGRAM_NAME to make it available again).
If you want to be able to quickly switch between different versions of the same program, use
/usr/local/stow/PROGRAM_NAME-VERSION as the program directory. To upgrade from version 3 to version 4, install version 4, then run
stow -D PROGRAM_NAME-3; stow PROGRAM_NAME-4.
Older versions of Stow doesn't go very far beyond the basics I've described in this answer. Newer versions, as well as XStow (which hasn't been maintained lately) have more advanced features, like the ability to ignore certain files, better cope with existing symlinks outside the stow directory (such as
man -> share/man), handle some conflicts automatically (when two programs provide the same file), etc.
If you don't have or don't want to use root access, you can pick a directory under your home directory, e.g.
~/software/stow. In this case, add
~/software/bin to your
man doesn't automatically find man pages, add
~/software/man to your
~/software/info to your
~/software/lib/python to your
PYTHONPATH, and so on as applicable.