[trunk] Fix invalid write access in JPIP code.

Fixes issue 261
[trunk] Properly store and use value returned by fread. Also invert nmemb and size in fread call.

Fixes issue 262
[trunk] Remove simple warnings about unused functions
[trunk] regex would not be used to remove java deprecation warning from dashboard
[trunk] Fix TestJPIP1 on case sensitive system
[trunk] Clearly indicate that mem-b2ace68c-1381.jp2 should not be decompressed.

Update issue 250