FASTQ files are not always stored in the expected folder

[Nicklas Nordborg]

Expected:

6605909.1/l.r.m2.c.lib.g
6605909.2/l.r.m2.c.lib.g
SKBR3/m.c.lib.g
Stratagene/r001.m10.c.lib
External/r.m55.c.lib.g
External/r.m99.c.lib.g

Actual:

6605909.1/l.r.m2.c.lib.g
6605909.2/l.r.m2.c.lib.g
SKBR3.m.c/lib.g
Stratagene.r001.m10.c/lib
External.r.m99.c/lib.g

This difference is also mapped to the folder structure in the BASE file system but it is even more messed up.

[Nicklas Nordborg]

(In [2773]) References #656: FASTQ files are not always stored in the expected folder

This should fix the problem on the project archive. Instead of looking for '.l' and replacing it with '/l', we now look for 'the first dot not followed by a digit' and replace that with '/'.

[Nicklas Nordborg]

(In [2779]) Fixes #656: FASTQ files are not always stored in the expected folder

Fixed the paths in the BASE file system. It will generate two extra 'prefix' levels for paths that has 7+1 digits in the first folder. Eg. /1234567.1/ --> /12/1234/1234567.1/

Ohter paths are not modified.

[Nicklas Nordborg]

(In [2802]) References #656: FASTQ files are not always stored in the expected folder

Same change in the CufflinksServlet as for the other servlets .