Add an application to the command search path in csh

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.

It turned out that lightdm (the login manager LXDE now uses) does not source ~/.profile.

What worked for me was creating ~/.xsessionrc:

if [ -d $HOME/bin ]; then
    export PATH="$HOME/bin:$PATH"
fi

You can also add this to /etc/X11/Xsession.d/90userbinpath if you want all user to benefit from this (each user would benefit for his own path) with a system-wide configuration.