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I found that /usr/lib/firefox-addons/plugins will be detected by firefox, but not by seamonkey (or, I'm guessing, other mozilla derivatives).
This was important to me as the 64-bit flash plugin was interfering with the 32-bit plugin I find I need for the latest version of seamonkey under ubuntu.
I now have the 64-bit flash in the above mentioned directory.
The 32-bit flash in ~/.mozilla/plugins
You might find that you have downgraded your flash player by cleaning that directory. You can see the versions of your plugins under Firefox by typing into the address bar:
about:plugins
You should definitely be running a version 10.x flash plugin.
I use the per-user libraries to prevent Seamonkey from attempting to run the 64-bit flash plugin. It works for me, but if you are likely to leave old versions in the directory and forget about it, you are probably best off clearing the directory and living with the support that comes in the standard packages which install into the /usr/... tree.
The /home/<user>/.mozilla/plugins directory is a per-user source of libraries which should override the system libraries. Unless you are doing something special, you are probably not going to want to use that directory. On the other hand, if you recall doing a bunch of work on your browser setup, clearing that directory might give you new opportunities for adventure.
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