Fix "`&' interpreted as argument prefix" warning in command.rb.

Cherry-pick of c4657940b18dfb3222be9905c1e561a5956d024b.
Fix "@" substitution in command-line arguments.
Merge branch 'master' into absolute-paths
Rename Package attribute "base_directory" to "include_file_base_directory".
Fix issues identified by «ruby -w -T1 -c».

Thank you Syntastic!
Merge branch 'master' into absolute-paths