A new installation will automatically install in /usr/local/ whilst your symbolic links are pointing to the installation in /usr/. The initial installation will therefoer not update your ruby version, unless you specify it everytime.
In order to make ruby 1.8.7 the default the symbolic links for ruby/gem/irb/erb/rake all need to be updated. Then all gems will need to be reinstalled, and indeed the passenger configuration in apache will need to be updated.
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