No longer implement deprecated handleNoSuchMethodError()

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Future-proof the IJ1Patcher

We will re-structure ij-legacy in a rather major way soon. The
LegacyExtensions class will lose its setters and configurations will be
performed exclusively by implementing SciJava-common plugins of certain
types (such as LegacyEditor, LegacyAppConfiguration, etc).

This is step one in the transition: use Javassist to access the current
methods to configure the patching.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Temporarily override the ij-legacy version we depend on

To provide forward-compatibility (support the new ij-legacy while keeping
a fallback to using the old ij-legacy as long as the update sites disagree
on versions), let's depend on an intermediate version of ij-legacy cut
specificially for fiji-compat's benefit.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Move some methods into FijiTools

They were in the Main class only out of historical reasons.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Use the shiny new ij1-patcher way to initialize

We have a new and improved way to initialize the legacy environment. The
code has been factored out into its own project, ij1-patcher, and we use
that, plus ij-legacy.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Document fiji.Main

While at it, deprecate a bunch of stuff.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fiji-compat depends on ij1-patcher now

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fiji-compat no longer depends on Javassist

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'ij1-patcher'

Conflicts:
	pom.xml

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Use ij1-patcher 0.1.1 in fiji-compat

The most critical bug fix in 0.1.1 is to work around batik.jar
previously shadowing xalan.jar's classes in some setup; That caused
a problem in tests graciously performed by Mark Hiner.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Clarify the temporary nature of the hardcoded versions in fiji-compat's pom

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fiji-compat: override the legacy editor with the Fiji one

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix deadlock with the EDT while opening the legacy editor

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update to Bio-Formats 5.0.0 release

While the artifact organization was restructured, the API is unchanged.
Include Bio-Formats in external artifacts list

It was already being pulled in transitively from Stitching, but
really, we want Bio-Formats to be bundled with Fiji in any case.
POM: fix typo in artifact exclusion
gitignore: update ignore list for Bio-Formats 5
gitignore: update ignore list further

Aside from the changes for Bio-Formats 5, there were
also several other JARs missing from the ignore list.
Let Simple Neurite Tracer work with newer JUnit

The assumeNotNull() function now takes a vararg and assumes that *all*
of the passed parameters should be null...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of github.com:fiji/fiji