further 11955 BF doc fixes & tidying
Fix missing bioformats_package.jar in bftools.zip

The jar was only present locally in the tools directory
since I had a symlink for testing. In the vanilla builds,
this change is necessary to prevent:

```
-rw-r--r-- 1 jamoore jamoore 16277709 Feb 10 20:36 artifacts/bioformats_package.jar
(ome1)jamoore@blue:/opt/ome3/components/bioformats$ ant dist-bftools
Buildfile: /opt/ome3/components/bioformats/build.xml

dist-bftools:
     [echo] ----------=========== bftools ===========----------
     [exec]     zip warning: name not matched: bioformats_package.jar
...

BUILD SUCCESSFUL
Total time: 0 seconds
```
update download link in sidebar menu
Fix upgrade checker to delete loci_tools.jar when appropriate

If bioformats_package.jar is requested but loci_tools.jar is present,
then loci_tools.jar is deleted (so that only one jar is present).
Fix whitespace in package jar location definition
merge dev_5_0 -D org -I include -E exclude: PR 900 (11955 further docs fixes)
merge dev_5_0 -D org -I include -E exclude: PR 901 (Fix missing bioformats_package.jar in bftools.zip)
merge dev_5_0 -D org -I include -E exclude: PR 903 (Fix upgrade checker to delete loci_tools.jar when appropriate)
merge dev_5_0 -D org -I include -E exclude: PR 904 (ITK: Fix whitespace in package jar location definition)