clean up template directory structure

[russ]

1. get rid of the journals/plosJournals directory (which is used as the location of site-wide freemarker template overrides) and replace it with the default journal's template directory.

why:

• the default journal's default.xml is used as the site-wide configuration override. it doesn't make sense to have the config override in one location and the freemarker template override in another.
• the existence of a random folder named "plosJournals" is an abomination

2. simplify the template directory structure

we can move the overlay journal's config file into the main template directory, and get rid of all the nested directory hierarchy above the actual template directory.

[rcave]

Moving out of 0.9.2 and into 0.9.3 as part of the template cleanup.

[rcave]

Moved to 0.9.3_rc2

[npeterson]

template cleanup rescheduled for 0.9.3_rc3

[dragisak]

(In [7764]) Major refactoring of template mechanism.

1. Site-wide override moved from /webapp/journals/plosJournal to default journal.
2. Removed redundancies in config files
   • Remove <defaultJournalName>
   • Simplify <virtualJournals><default><journal>..</journal><mappingprefix>...</mappingPrefix> to <virtualJournals><default>default-journal-name</default>
3. Add site-wide override for resources (images, css, javascript)

Addresses #1088 and #930

[dragisak]

(In [7767]) Apply changes in default journal configuration.

Should have been part of r7764

Addresses #1088