dependencies and dependencies-on dirs do not cleanup upon update

[ar13pit]

If the dependencies of packages have changed or certain packages are no longer installed, then their dependencies are still present in dependencies and dependencies-on directories

[MatthijsBurgh]

I think only in the dependencies-on files, not in the dependencies file, see

tue-env/installer/tue-install-impl.bash

Lines 198 to 200 in 871cacf

	# Empty the target's dependency file
	tue-install-debug "Emptying $TUE_INSTALL_DEPENDENCIES_DIR/$target"
	truncate -s 0 "$TUE_INSTALL_DEPENDENCIES_DIR"/"$target"