Patch for CellProfiler issue 1043 - Cellomics files with renamed filenames
Remove Eclipse metadata file

This file clashes with Eclipse when importing Bio-Formats via the
recommended "File > Import > Existing Maven Projects" mechanism.

Eclipse works after doing that, but it overwrites this .project file
with different contents, which makes Git always think there are local
changes, which affects rebase workflows.
First round of changing loci_tools to bioformats_package
Change CMake variable name
Minor change in docs of InstallWizard
Fix URL for download
Misc naming changes
Include bf_package.jar in bftools.zip
Doc suggestions from melissalinkert
Fix whitespace in package jar location definition
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
```
Flatten path to bioformats_package.jar in bftools.zip (see gh-901)

Since this uses the native zip command, invoking from the
artifact.dir seems to be the most portable way to get the
unprefixed jar into the zip.
Fix updater menu item to match window title
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).
further 11955 BF doc fixes & tidying
update download link in sidebar menu
sorting index and installation guide
Further tidying from Roger
Removing out of date version & milestone info
Use corrected download redirects for 5