RDoc ri store update corrupts visibility information

[gettalong]

When creating an RDoc ri store and then later updating it, the visibility information is corrupted, ie. public or protected methods are shown as private methods.

Steps to reproduce (should be possible to reproduce with any Ruby files but for convenience):

$ git clone git@github.com:gettalong/cmdparse.git
$ cd cmdparse
$ rdoc -v
4.2.0
$ rdoc --op rdoc-op --ri --quiet lib                                              
$ grep public rdoc-op/CmdParse/CommandParser/parse-i.ri                          
Binary file rdoc-op/CmdParse/CommandParser/parse-i.ri matches
$ rdoc --op rdoc-op --ri --quiet lib
$ grep public rdoc-op/CmdParse/CommandParser/parse-i.ri 
$ grep private rdoc-op/CmdParse/CommandParser/parse-i.ri 
Binary file rdoc-op/CmdParse/CommandParser/parse-i.ri matches

[zzak]

This is really strange, maybe easier to debug if we can get a failing test for it.

I'll see what I can do.