Add multiple subdirectories under the same parent directory to PATH

Adding a directory to PATH only makes the executables in this directory available as bare command names. This does not extend to subdirectories.

You can put a loop in your .profile (not .bashrc) to add multiple directories, for example:

for d in ~/tools/*/bin; do
  PATH="$PATH:$d"
done

(You don't need to repeat export: when a variable is exported, it stays exported, and modifications are reflected in the environment).

If you create new directories under tools, this will not be reflected in your ongoing session, only the next time .profile is read. If this is not satisfactory, you can use a different approach: put a single directory such as ~/bin in your PATH, and when you install software, create symbolic links in ~/bin. Stow (or its alternative XStow) is a good way of doing this; see Keeping track of programs for an overview of how this works.