Add build-environment mojo

[frauzufall]

Goal: create a mojo to build a scijava based app from scratch (e.g. by running the mojo in the fiji/fiji repository)

[frauzufall]

I just copied the copy-jars mojo so far. Built the app by running mvn -Dscijava.app.directory=/PATH/TO/Fiji.build org.scijava:scijava-maven-plugin:1.1.2-SNAPSHOT:build-environment on the fiji/fiji master branch. Here's the comparison to the currently downloadable Fiji (linux64, Fiji.app is the downloaded one, Fiji.build the one built from the mojo):

Comparing via diff -r Fiji.build Fiji.app

```ssh (base) ➜ build-environment diff -r Fiji.build Fiji.app Only in Fiji.app: Contents Only in Fiji.app: db.xml.gz Only in Fiji.app: ImageJ-linux64 Only in Fiji.app: images Only in Fiji.app/jars: asm-analysis-4.0.jar Only in Fiji.app/jars: autocomplete-2.6.1.jar Only in Fiji.build/jars: autocomplete-3.0.0.jar Only in Fiji.app/jars: batik-anim-1.10.jar Only in Fiji.build/jars: batik-anim-1.11.jar Only in Fiji.app/jars: batik-awt-util-1.10.jar Only in Fiji.build/jars: batik-awt-util-1.11.jar Only in Fiji.app/jars: batik-bridge-1.10.jar Only in Fiji.build/jars: batik-bridge-1.11.jar Only in Fiji.app/jars: batik-constants-1.10.jar Only in Fiji.build/jars: batik-constants-1.11.jar Only in Fiji.app/jars: batik-css-1.10.jar Only in Fiji.build/jars: batik-css-1.11.jar Only in Fiji.app/jars: batik-dom-1.10.jar Only in Fiji.build/jars: batik-dom-1.11.jar Only in Fiji.app/jars: batik-ext-1.10.jar Only in Fiji.build/jars: batik-ext-1.11.jar Only in Fiji.app/jars: batik-gvt-1.10.jar Only in Fiji.build/jars: batik-gvt-1.11.jar Only in Fiji.app/jars: batik-i18n-1.10.jar Only in Fiji.build/jars: batik-i18n-1.11.jar Only in Fiji.app/jars: batik-parser-1.10.jar Only in Fiji.build/jars: batik-parser-1.11.jar Only in Fiji.app/jars: batik-script-1.10.jar Only in Fiji.build/jars: batik-script-1.11.jar Only in Fiji.app/jars: batik-svg-dom-1.10.jar Only in Fiji.build/jars: batik-svg-dom-1.11.jar Only in Fiji.app/jars: batik-svggen-1.10.jar Only in Fiji.build/jars: batik-svggen-1.11.jar Only in Fiji.app/jars: batik-util-1.10.jar Only in Fiji.build/jars: batik-util-1.11.jar Only in Fiji.app/jars: batik-xml-1.10.jar Only in Fiji.build/jars: batik-xml-1.11.jar Only in Fiji.build/jars: bigdataviewer_fiji-6.0.0.jar Only in Fiji.build/jars/bio-formats: formats-api-6.3.0.jar Only in Fiji.app/jars/bio-formats: formats-api-6.4.0.jar Only in Fiji.build/jars/bio-formats: formats-bsd-6.3.0.jar Only in Fiji.app/jars/bio-formats: formats-bsd-6.4.0.jar Only in Fiji.build/jars/bio-formats: formats-gpl-6.3.0.jar Only in Fiji.app/jars/bio-formats: formats-gpl-6.4.0.jar Only in Fiji.app/jars/bio-formats: jai_imageio-5.1.10.jar Only in Fiji.build/jars/bio-formats: jxrlib-all-0.2.1.jar Only in Fiji.app/jars/bio-formats: jxrlib-all-0.2.2.jar Only in Fiji.app/jars/bio-formats: metakit-5.3.2.jar Only in Fiji.app/jars/bio-formats: ome-codecs-0.3.0.jar Only in Fiji.app/jars/bio-formats: ome-common-6.0.4.jar Only in Fiji.app/jars/bio-formats: ome-jai-0.1.0.jar Only in Fiji.app/jars/bio-formats: ome-mdbtools-5.3.2.jar Only in Fiji.app/jars/bio-formats: ome-poi-5.3.3.jar Only in Fiji.app/jars/bio-formats: ome-xml-6.0.1.jar Only in Fiji.app/jars/bio-formats: specification-6.0.1.jar Only in Fiji.build/jars/bio-formats: turbojpeg-6.3.0.jar Only in Fiji.app/jars/bio-formats: turbojpeg-6.4.0.jar Only in Fiji.build/jars: c3p0-0.9.5.3.jar Only in Fiji.build/jars: cdm-4.6.13.jar Only in Fiji.app/jars: commons-codec-1.11.jar Only in Fiji.build/jars: commons-codec-1.12.jar Only in Fiji.build/jars: commons-compress-1.18.jar Only in Fiji.app/jars: commons-compress-1.4.1.jar Only in Fiji.app/jars: commons-httpclient-3.1.jar Only in Fiji.app/jars: commons-lang3-3.8.1.jar Only in Fiji.build/jars: commons-lang3-3.9.jar Only in Fiji.build/jars: commons-text-1.6.jar Only in Fiji.build/jars: Correct_3D_Drift-1.0.3.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-android-arm64.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-android-arm.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-android-x86_64.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-android-x86.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-linux-armhf.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-linux-ppc64le.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-linux-x86_64.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-linux-x86.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-macosx-x86_64.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-windows-x86_64.jar Only in Fiji.build/jars: ffmpeg-4.1-1.4.4-windows-x86.jar Only in Fiji.app/jars: fiji-2.0.0-pre-8.jar Only in Fiji.build/jars: fiji-2.0.0-SNAPSHOT.jar Only in Fiji.app/jars: fiji-compat-2.0.3.jar Only in Fiji.app/jars: gentyref-1.1.0.jar Only in Fiji.app/jars: gluegen-rt-2.3.2.jar Only in Fiji.build/jars: gluegen-rt-2.3.2-natives-android-aarch64.jar Only in Fiji.build/jars: google-http-client-1.20.0.jar Only in Fiji.build/jars: google-http-client-xml-1.20.0.jar Only in Fiji.app/jars: groovy-json-2.4.8.jar Only in Fiji.app/jars: groovy-templates-2.4.8.jar Only in Fiji.app/jars: groovy-xml-2.4.8.jar Only in Fiji.build/jars: httpclient-4.5.1.jar Only in Fiji.app/jars: httpclient-4.5.6.jar Only in Fiji.app/jars: httpcore-4.4.11.jar Only in Fiji.build/jars: httpmime-4.5.1.jar Only in Fiji.build/jars: httpservices-4.6.13.jar Only in Fiji.app/jars: ij-1.52p.jar Only in Fiji.build/jars: ij-1.52r.jar Only in Fiji.app/jars: ij1-patcher-0.12.9.jar Only in Fiji.build/jars: ij1-patcher-1.0.0.jar Only in Fiji.app/jars: imagej-2.0.0-rc-69.jar Only in Fiji.build/jars: imagej-2.0.0-rc-72.jar Only in Fiji.app/jars: imagej-common-0.28.2.jar Only in Fiji.build/jars: imagej-common-0.31.0.jar Only in Fiji.app/jars: imagej-launcher-4.0.5.jar Only in Fiji.build/jars: imagej-legacy-0.35.0.jar Only in Fiji.app/jars: imagej-legacy-0.35.2.jar Only in Fiji.app/jars: imagej-mesh-io-0.1.2.jar Only in Fiji.app/jars: imagej-notebook-0.3.0.jar Only in Fiji.build/jars: imagej-notebook-0.7.1.jar Only in Fiji.app/jars: imagej-ops-0.43.1.jar Only in Fiji.build/jars: imagej-ops-0.45.2.jar Only in Fiji.build/jars: imagej-plugins-uploader-webdav-0.2.2.jar Only in Fiji.app/jars: imagej-plugins-uploader-webdav-0.3.1.jar Only in Fiji.build/jars: imagej-ui-swing-0.22.0.jar Only in Fiji.app/jars: imagej-ui-swing-0.23.1.jar Only in Fiji.app/jars: imagej-updater-0.10.4.jar Only in Fiji.build/jars: imagej-updater-0.9.3.jar Only in Fiji.app/jars: imglib2-5.6.3.jar Only in Fiji.build/jars: imglib2-5.8.0.jar Only in Fiji.app/jars: imglib2-roi-0.7.0.jar Only in Fiji.build/jars: imglib2-roi-0.8.1.jar Only in Fiji.build/jars: itextpdf-5.5.13.1.jar Only in Fiji.app/jars: itextpdf-5.5.13.jar Only in Fiji.app/jars: jackrabbit-webdav-2.19.1.jar Only in Fiji.build/jars: jackson-annotations-2.9.8.jar Only in Fiji.build/jars: jackson-core-2.9.8.jar Only in Fiji.build/jars: jackson-databind-2.9.8.jar Only in Fiji.app/jars: javassist-3.24.0-GA.jar Only in Fiji.build/jars: javassist-3.25.0-GA.jar Only in Fiji.app/jars: jcommon-1.0.24.jar Binary files Fiji.build/jars/jep-2.4.2.jar and Fiji.app/jars/jep-2.4.2.jar differ Only in Fiji.build/jars: jfreesvg-3.4.jar Only in Fiji.app/jars: jgrapht-0.0.0-STUB.jar Only in Fiji.app/jars: jgrapht-core-1.3.0.jar Only in Fiji.build/jars: jgrapht-core-1.3.1.jar Only in Fiji.build/jars: jheaps-0.10.jar Only in Fiji.app/jars: jheaps-0.9.jar Only in Fiji.app/jars: jitk-tps-3.0.0.jar Only in Fiji.build/jars: jitk-tps-3.0.1.jar Only in Fiji.app/jars: jnr-ffi-1.0.7.jar Only in Fiji.app/jars: joal-2.3.2.jar Only in Fiji.build/jars: joal-2.3.2-natives-android-aarch64.jar Only in Fiji.app/jars: jocl-2.3.2.jar Only in Fiji.build/jars: jocl-2.3.2-natives-android-aarch64.jar Only in Fiji.app/jars: joda-time-2.10.1.jar Only in Fiji.build/jars: joda-time-2.10.2.jar Only in Fiji.app/jars: jogl-all-2.3.2.jar Only in Fiji.build/jars: jogl-all-2.3.2-natives-android-aarch64.jar Only in Fiji.app/jars: joml-1.9.12.jar Only in Fiji.build/jars: joml-1.9.16.jar Only in Fiji.app/jars: jply-0.2.0.jar Only in Fiji.build/jars: jython-shaded-2.7.1.1.jar Only in Fiji.app/jars: jython-shaded-2.7.1.jar Only in Fiji.build/jars: KymographBuilder-2.1.1.jar Only in Fiji.app/jars: languagesupport-2.6.0.jar Only in Fiji.build/jars: languagesupport-3.0.0.jar Only in Fiji.app/jars: linux64 Only in Fiji.app/jars: mapdb-1.0.3.jar Only in Fiji.build/jars: mchange-commons-java-0.2.15.jar Only in Fiji.build/jars: metadata-extractor-2.11.0.jar Only in Fiji.app/jars: metadata-extractor-2.6.2.jar Only in Fiji.build/jars: metakit-5.3.2.jar Only in Fiji.app/jars: minimaven-2.2.1.jar Only in Fiji.build/jars: minimaven-2.2.2.jar Only in Fiji.build/jars: minio-5.0.2.jar Only in Fiji.app/jars: native-lib-loader-2.3.2.jar Only in Fiji.build/jars: native-lib-loader-2.3.4.jar Only in Fiji.app/jars: netcdf-4.3.22.jar Only in Fiji.build/jars: okhttp-3.6.0.jar Only in Fiji.build/jars: okio-1.11.0.jar Only in Fiji.build/jars: ome-codecs-0.2.5.jar Only in Fiji.build/jars: ome-common-6.0.4.jar Only in Fiji.build/jars: ome-jai-0.1.0.jar Only in Fiji.build/jars: ome-mdbtools-5.3.2.jar Only in Fiji.build/jars: ome-poi-5.3.3.jar Only in Fiji.build/jars: ome-xml-6.0.1.jar Only in Fiji.app/jars: perf4j-0.9.13.jar Only in Fiji.build/jars: perf4j-0.9.16.jar Only in Fiji.app/jars: rsyntaxtextarea-2.6.1.jar Only in Fiji.build/jars: rsyntaxtextarea-3.0.3.jar Only in Fiji.app/jars: scijava-common-2.80.1.jar Only in Fiji.build/jars: scijava-common-2.82.0.jar Only in Fiji.build/jars: scijava-io-http-0.2.0.jar Only in Fiji.build/jars: scijava-plugins-io-table-0.2.0.jar Only in Fiji.app/jars: scijava-search-0.5.0.jar Only in Fiji.build/jars: scijava-search-0.6.0.jar Only in Fiji.app/jars: scijava-table-0.2.0.jar Only in Fiji.build/jars: scijava-table-0.4.0.jar Only in Fiji.app/jars: scijava-ui-swing-0.12.0.jar Only in Fiji.build/jars: scijava-ui-swing-0.13.0.jar Only in Fiji.build/jars: script-editor-0.5.0.jar Only in Fiji.app/jars: script-editor-0.5.1.jar Only in Fiji.app/jars: serializer-2.7.2.jar Only in Fiji.app/jars: slf4j-api-1.7.25.jar Only in Fiji.build/jars: slf4j-api-1.7.26.jar Only in Fiji.app/jars: snakeyaml-1.23.jar Only in Fiji.build/jars: snakeyaml-1.24.jar Only in Fiji.build/jars: specification-6.0.1.jar Only in Fiji.app/jars: T2-NIT-1.1.2.jar Only in Fiji.build/jars: T2-NIT-1.1.3.jar Only in Fiji.app/jars: T2-TreelineGraph-1.1.2.jar Only in Fiji.build/jars: T2-TreelineGraph-1.1.3.jar Only in Fiji.build/jars: VectorGraphics2D-0.13.jar Only in Fiji.app/jars: xalan-2.7.2.jar Only in Fiji.build/jars: xchart-3.5.4.jar Only in Fiji.app/jars: xmpcore-5.1.2.jar Only in Fiji.build/jars: xmpcore-5.1.3.jar Only in Fiji.build/jars: xpp3-1.1.4c.jar Only in Fiji.app/jars: xz-1.0.jar Only in Fiji.app/jars: yecht-1.0.jar Only in Fiji.app: java Only in Fiji.app: lib Only in Fiji.app: luts Only in Fiji.app: macros Only in Fiji.app/plugins: Analyze Only in Fiji.app/plugins: AnalyzeSkeleton_-3.3.0.jar Only in Fiji.build/plugins: AnalyzeSkeleton_-3.4.1.jar Only in Fiji.app/plugins: bigdataviewer_fiji-6.0.0.jar Only in Fiji.build/plugins: bio-formats_plugins-6.3.0.jar Only in Fiji.app/plugins: bio-formats_plugins-6.4.0.jar Only in Fiji.build/plugins: bUnwarpJ_-2.6.11.jar Only in Fiji.app/plugins: bUnwarpJ_-2.6.12.jar Only in Fiji.app/plugins: Correct_3D_Drift-1.0.3.jar Only in Fiji.app/plugins: Examples Only in Fiji.app/plugins: JRuby Only in Fiji.app/plugins: KymographBuilder-2.1.1.jar Only in Fiji.app/plugins: Macros Only in Fiji.app/plugins: readme.txt Only in Fiji.build/plugins: register_virtual_stack_slices-3.0.5.jar Only in Fiji.app/plugins: register_virtual_stack_slices-3.0.7.jar Only in Fiji.app/plugins: Scripts Only in Fiji.build/plugins: Stack_Manipulation-2.1.1.jar Only in Fiji.app/plugins: Stack_Manipulation-2.1.2.jar Only in Fiji.build/plugins: TrackMate_-4.0.0.jar Only in Fiji.app/plugins: TrackMate_-5.2.0.jar Only in Fiji.build/plugins: Trainable_Segmentation-3.2.29.jar Only in Fiji.app/plugins: Trainable_Segmentation-3.2.34.jar Only in Fiji.app/plugins: Utilities Only in Fiji.app/plugins: Vaa3d_Writer-1.0.2.jar Only in Fiji.build/plugins: Vaa3d_Writer-1.0.3.jar Only in Fiji.app: README.md Only in Fiji.app: retro Only in Fiji.app: scripts Only in Fiji.app: WELCOME.md ```

[ctrueden]

@frauzufall Cool!

I think it would help a lot to do a color-words diff, rather than a normal line-by-line diff, because a lot of those differences are just version numbers. Those don't illustrate gaps in the mojo, but things like missing scripts and other resources, as well as JARs in the wrong place, do.

[frauzufall]

Yes.. I tried a couple of command line comparison tools but nothing was super helpful or colored.. I wrote a helper class a while ago for the maven updater prototype, it prints this (not bulletproof, but helpful):

file changes via CompareDirectories.java

```ssh Comparing /home/random/Development/imagej/project/updater/build-environment/Fiji.build with /home/random/Development/imagej/project/updater/build-environment/Fiji.app: ADDED /Contents/Info.plist ADDED /Contents/Resources/Fiji.icns ADDED /Contents/Resources/ImageJ.icns ADDED /ImageJ-linux64 ADDED /README.md ADDED /WELCOME.md ADDED /db.xml.gz ADDED /images/about/about1.tif ADDED /images/about/about1.tif.txt ADDED /images/about/about2.tif ADDED /images/about/about2.tif.txt ADDED /images/about/about3.tif ADDED /images/about/about3.tif.txt ADDED /images/about/about4.tif ADDED /images/about/about4.tif.txt ADDED /images/about/about5.tif ADDED /images/about/about5.tif.txt ADDED /images/icon-flat.png ADDED /images/icon.png ADDED /jars/asm-analysis-4.0.jar ADDED /jars/bio-formats/jai_imageio-5.1.10.jar ADDED /jars/bio-formats/ome-codecs-0.3.0.jar ADDED /jars/commons-httpclient-3.1.jar ADDED /jars/fiji-compat-2.0.3.jar ADDED /jars/gentyref-1.1.0.jar ADDED /jars/groovy-json-2.4.8.jar ADDED /jars/groovy-templates-2.4.8.jar ADDED /jars/groovy-xml-2.4.8.jar ADDED /jars/httpcore-4.4.11.jar ADDED /jars/imagej-launcher-4.0.5.jar ADDED /jars/imagej-mesh-io-0.1.2.jar ADDED /jars/jackrabbit-webdav-2.19.1.jar ADDED /jars/jcommon-1.0.24.jar ADDED /jars/jgrapht-0.0.0-STUB.jar ADDED /jars/jnr-ffi-1.0.7.jar ADDED /jars/jply-0.2.0.jar ADDED /jars/linux64/gluegen-rt-2.3.2-natives-linux-amd64.jar ADDED /jars/linux64/joal-2.3.2-natives-linux-amd64.jar ADDED /jars/linux64/jocl-2.3.2-natives-linux-amd64.jar ADDED /jars/linux64/jogl-all-2.3.2-natives-linux-amd64.jar ADDED /jars/mapdb-1.0.3.jar ADDED /jars/netcdf-4.3.22.jar ADDED /jars/serializer-2.7.2.jar ADDED /jars/xalan-2.7.2.jar ADDED /jars/xz-1.0.jar ADDED /jars/yecht-1.0.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/COPYRIGHT ADDED /java/linux-amd64/jdk1.8.0_172/jre/LICENSE ADDED /java/linux-amd64/jdk1.8.0_172/jre/README ADDED /java/linux-amd64/jdk1.8.0_172/jre/THIRDPARTYLICENSEREADME-JAVAFX.txt ADDED /java/linux-amd64/jdk1.8.0_172/jre/THIRDPARTYLICENSEREADME.txt ADDED /java/linux-amd64/jdk1.8.0_172/jre/Welcome.html ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/ControlPanel ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/java ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/javaws ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/jcontrol ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/jjs ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/keytool ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/orbd ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/pack200 ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/policytool ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/rmid ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/rmiregistry ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/servertool ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/tnameserv ADDED /java/linux-amd64/jdk1.8.0_172/jre/bin/unpack200 ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/jli/libjli.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/jvm.cfg ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-53.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-54.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-55.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-56.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-57.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-ffmpeg-56.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libavplugin-ffmpeg-57.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libawt.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libawt_headless.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libawt_xawt.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libbci.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libdcpr.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libdecora_sse.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libdeploy.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libdt_socket.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libfontmanager.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libfxplugins.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libglass.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libgstreamer-lite.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libhprof.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libinstrument.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libj2gss.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libj2pcsc.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libj2pkcs11.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjaas_unix.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjava.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjava_crw_demo.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjavafx_font.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjavafx_font_freetype.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjavafx_font_pango.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjavafx_font_t2k.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjavafx_iio.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjawt.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjdwp.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjfr.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjfxmedia.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjfxwebkit.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjpeg.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjsdt.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjsig.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjsound.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libjsoundalsa.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libkcms.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/liblcms.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libmanagement.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libmlib_image.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libnet.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libnio.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libnpjp2.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libnpt.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libprism_common.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libprism_es2.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libprism_sw.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libresource.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libsctp.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libsplashscreen.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libsunec.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libt2k.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libunpack.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libverify.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/libzip.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/server/Xusage.txt ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/server/libjsig.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/amd64/server/libjvm.so ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/calendars.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/charsets.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/classlist ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/cmm/CIEXYZ.pf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/cmm/GRAY.pf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/cmm/LINEAR_RGB.pf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/cmm/PYCC.pf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/cmm/sRGB.pf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/content-types.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/currency.data ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/MixedCodeMainDialog.ui ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/MixedCodeMainDialogJs.ui ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/cautionshield.icns ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/ffjcext.zip ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/java-icon.ico ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_de.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_es.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_fr.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_it.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_ja.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_ko.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_pt_BR.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_sv.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_zh_CN.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_zh_HK.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/messages_zh_TW.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/mixcode_s.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/splash.gif ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/splash@2x.gif ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/splash_11-lic.gif ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/deploy/splash_11@2x-lic.gif ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/applications/sun-java.desktop ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/applications/sun-javaws.desktop ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/applications/sun_java.desktop ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/16x16/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrast/48x48/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/16x16/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/HighContrastInverse/48x48/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/16x16/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/LowContrast/48x48/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/16x16/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/apps/sun-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/apps/sun-javaws.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/apps/sun-jcontrol.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/mimetypes/gnome-mime-application-x-java-archive.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/mimetypes/gnome-mime-application-x-java-jnlp-file.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/icons/hicolor/48x48/mimetypes/gnome-mime-text-x-java.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/mime/packages/x-java-archive.xml ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/desktop/mime/packages/x-java-jnlp-file.xml ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/cldrdata.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/dnsns.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/jaccess.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/jfxrt.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/localedata.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/meta-index ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/nashorn.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/sunec.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/sunjce_provider.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/sunpkcs11.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/ext/zipfs.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/flavormap.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.RedHat.5.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.RedHat.5.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.RedHat.6.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.RedHat.6.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.SuSE.10.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.SuSE.10.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.SuSE.11.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.SuSE.11.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.Turbo.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.Turbo.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.bfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fontconfig.properties.src ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaBrightDemiBold.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaBrightDemiItalic.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaBrightItalic.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaBrightRegular.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaSansDemiBold.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaSansRegular.ttf ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/fonts/LucidaTypewriterBold.ttf ADDED 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/java/linux-amd64/jdk1.8.0_172/jre/lib/images/icons/sun-java_HighContrast.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/images/icons/sun-java_HighContrastInverse.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/images/icons/sun-java_LowContrast.png ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/javafx.properties ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/javaws.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jce.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jexec ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jfr.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jfr/default.jfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jfr/profile.jfc ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jfxswt.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jsse.jar ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/jvm.hprof.txt ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/locale/de/LC_MESSAGES/sunw_java_plugin.mo ADDED /java/linux-amd64/jdk1.8.0_172/jre/lib/locale/es/LC_MESSAGES/sunw_java_plugin.mo ADDED 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/java/linux-amd64/jdk1.8.0_172/jre/man/ja/man1/tnameserv.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja/man1/unpack200.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/java.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/javaws.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/jjs.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/keytool.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/orbd.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/pack200.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/policytool.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/rmid.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/rmiregistry.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/servertool.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/tnameserv.1 ADDED /java/linux-amd64/jdk1.8.0_172/jre/man/ja_JP.UTF-8/man1/unpack200.1 ADDED 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/plugins/Scripts/Plugins/AutoRun/Check_Required_Update_Sites.js ADDED /plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh ADDED /plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh ADDED /plugins/Scripts/Plugins/Utilities/Record_Desktop.py ADDED /plugins/Scripts/Plugins/Utilities/Record_Window.py ADDED /plugins/Utilities/Close_All_Without_Saving.txt ADDED /plugins/readme.txt ADDED /retro/backport-util-concurrent-3.1.jar ADDED /retro/retrotranslator-runtime-1.2.9.jar ADDED /retro/retrotranslator-transformer-1.2.9.jar ADDED /scripts/ImageJ.m ADDED /scripts/InstallJava3D.m ADDED /scripts/IsJava3DInstalled.m ADDED /scripts/Matlab3DViewerDemo_1.m ADDED /scripts/Matlab3DViewerDemo_2.m ADDED /scripts/Matlab3DViewerDemo_3.m ADDED /scripts/Matlab3DViewerIntroduction.m ADDED /scripts/Miji.m ADDED /scripts/Miji_Test.m ADDED /scripts/bfopen.m ADDED /scripts/copytoImg.m ADDED /scripts/copytoImgPlus.m ADDED /scripts/copytoMatlab.m ADDED /scripts/importTrackMateTracks.m ADDED /scripts/trackmateEdges.m ADDED /scripts/trackmateFeatureDeclarations.m ADDED /scripts/trackmateGraph.m ADDED /scripts/trackmateImageCalibration.m ADDED /scripts/trackmateSpots.m DELETED /jars/VectorGraphics2D-0.13.jar DELETED /jars/c3p0-0.9.5.3.jar DELETED /jars/cdm-4.6.13.jar DELETED /jars/commons-text-1.6.jar DELETED /jars/ffmpeg-4.1-1.4.4-android-arm.jar DELETED /jars/ffmpeg-4.1-1.4.4-android-arm64.jar DELETED /jars/ffmpeg-4.1-1.4.4-android-x86.jar DELETED /jars/ffmpeg-4.1-1.4.4-android-x86_64.jar DELETED /jars/ffmpeg-4.1-1.4.4-linux-armhf.jar DELETED /jars/ffmpeg-4.1-1.4.4-linux-ppc64le.jar DELETED /jars/ffmpeg-4.1-1.4.4-linux-x86.jar DELETED /jars/ffmpeg-4.1-1.4.4-macosx-x86_64.jar DELETED /jars/ffmpeg-4.1-1.4.4-windows-x86.jar DELETED /jars/ffmpeg-4.1-1.4.4-windows-x86_64.jar DELETED /jars/google-http-client-1.20.0.jar DELETED /jars/google-http-client-xml-1.20.0.jar DELETED /jars/httpmime-4.5.1.jar DELETED /jars/httpservices-4.6.13.jar DELETED /jars/jackson-annotations-2.9.8.jar DELETED /jars/jackson-core-2.9.8.jar DELETED /jars/jackson-databind-2.9.8.jar DELETED /jars/jfreesvg-3.4.jar DELETED /jars/mchange-commons-java-0.2.15.jar DELETED /jars/minio-5.0.2.jar DELETED /jars/okhttp-3.6.0.jar DELETED /jars/okio-1.11.0.jar DELETED /jars/ome-codecs-0.2.5.jar DELETED /jars/scijava-io-http-0.2.0.jar DELETED /jars/scijava-plugins-io-table-0.2.0.jar DELETED /jars/xchart-3.5.4.jar DELETED /jars/xpp3-1.1.4c.jar MODIFED /jars/jep-2.4.2.jar -> /jars/jep-2.4.2.jar VERSION_CHANGED /jars/T2-NIT (1.1.3 -> 1.1.2) VERSION_CHANGED /jars/T2-TreelineGraph (1.1.3 -> 1.1.2) VERSION_CHANGED /jars/autocomplete (3.0.0 -> 2.6.1) VERSION_CHANGED /jars/batik-anim (1.11 -> 1.10) VERSION_CHANGED /jars/batik-awt-util (1.11 -> 1.10) VERSION_CHANGED /jars/batik-bridge (1.11 -> 1.10) VERSION_CHANGED /jars/batik-constants (1.11 -> 1.10) VERSION_CHANGED /jars/batik-css (1.11 -> 1.10) VERSION_CHANGED /jars/batik-dom (1.11 -> 1.10) VERSION_CHANGED /jars/batik-ext (1.11 -> 1.10) VERSION_CHANGED /jars/batik-gvt (1.11 -> 1.10) VERSION_CHANGED /jars/batik-i18n (1.11 -> 1.10) VERSION_CHANGED /jars/batik-parser (1.11 -> 1.10) VERSION_CHANGED /jars/batik-script (1.11 -> 1.10) VERSION_CHANGED /jars/batik-svg-dom (1.11 -> 1.10) VERSION_CHANGED /jars/batik-svggen (1.11 -> 1.10) VERSION_CHANGED /jars/batik-util (1.11 -> 1.10) VERSION_CHANGED /jars/batik-xml (1.11 -> 1.10) VERSION_CHANGED /jars/bio-formats/formats-api (6.3.0 -> 6.4.0) VERSION_CHANGED /jars/bio-formats/formats-bsd (6.3.0 -> 6.4.0) VERSION_CHANGED /jars/bio-formats/formats-gpl (6.3.0 -> 6.4.0) VERSION_CHANGED /jars/bio-formats/jxrlib-all (0.2.1 -> 0.2.2) VERSION_CHANGED /jars/bio-formats/turbojpeg (6.3.0 -> 6.4.0) VERSION_CHANGED /jars/commons-codec (1.12 -> 1.11) VERSION_CHANGED /jars/commons-compress (1.18 -> 1.4.1) VERSION_CHANGED /jars/commons-lang3 (3.9 -> 3.8.1) VERSION_CHANGED /jars/fiji (2.0.0-SNAPSHOT -> 2.0.0-pre-8) VERSION_CHANGED /jars/gluegen-rt (2.3.2-natives-android-aarch64 -> 2.3.2) VERSION_CHANGED /jars/httpclient (4.5.1 -> 4.5.6) VERSION_CHANGED /jars/ij (1.52r -> 1.52p) VERSION_CHANGED /jars/ij1-patcher (1.0.0 -> 0.12.9) VERSION_CHANGED /jars/imagej (2.0.0-rc-72 -> 2.0.0-rc-69) VERSION_CHANGED /jars/imagej-common (0.31.0 -> 0.28.2) VERSION_CHANGED /jars/imagej-legacy (0.35.0 -> 0.35.2) VERSION_CHANGED /jars/imagej-notebook (0.7.1 -> 0.3.0) VERSION_CHANGED /jars/imagej-ops (0.45.2 -> 0.43.1) VERSION_CHANGED /jars/imagej-plugins-uploader-webdav (0.2.2 -> 0.3.1) VERSION_CHANGED /jars/imagej-ui-swing (0.22.0 -> 0.23.1) VERSION_CHANGED /jars/imagej-updater (0.9.3 -> 0.10.4) VERSION_CHANGED /jars/imglib2 (5.8.0 -> 5.6.3) VERSION_CHANGED /jars/imglib2-roi (0.8.1 -> 0.7.0) VERSION_CHANGED /jars/itextpdf (5.5.13.1 -> 5.5.13) VERSION_CHANGED /jars/javassist (3.25.0-GA -> 3.24.0-GA) VERSION_CHANGED /jars/jgrapht-core (1.3.1 -> 1.3.0) VERSION_CHANGED /jars/jheaps (0.10 -> 0.9) VERSION_CHANGED /jars/jitk-tps (3.0.1 -> 3.0.0) VERSION_CHANGED /jars/joal (2.3.2-natives-android-aarch64 -> 2.3.2) VERSION_CHANGED /jars/jocl (2.3.2-natives-android-aarch64 -> 2.3.2) VERSION_CHANGED /jars/joda-time (2.10.2 -> 2.10.1) VERSION_CHANGED /jars/jogl-all (2.3.2-natives-android-aarch64 -> 2.3.2) VERSION_CHANGED /jars/joml (1.9.16 -> 1.9.12) VERSION_CHANGED /jars/jython-shaded (2.7.1.1 -> 2.7.1) VERSION_CHANGED /jars/languagesupport (3.0.0 -> 2.6.0) VERSION_CHANGED /jars/metadata-extractor (2.11.0 -> 2.6.2) VERSION_CHANGED /jars/minimaven (2.2.2 -> 2.2.1) VERSION_CHANGED /jars/native-lib-loader (2.3.4 -> 2.3.2) VERSION_CHANGED /jars/perf4j (0.9.16 -> 0.9.13) VERSION_CHANGED /jars/rsyntaxtextarea (3.0.3 -> 2.6.1) VERSION_CHANGED /jars/scijava-common (2.82.0 -> 2.80.1) VERSION_CHANGED /jars/scijava-search (0.6.0 -> 0.5.0) VERSION_CHANGED /jars/scijava-table (0.4.0 -> 0.2.0) VERSION_CHANGED /jars/scijava-ui-swing (0.13.0 -> 0.12.0) VERSION_CHANGED /jars/script-editor (0.5.0 -> 0.5.1) VERSION_CHANGED /jars/slf4j-api (1.7.26 -> 1.7.25) VERSION_CHANGED /jars/snakeyaml (1.24 -> 1.23) VERSION_CHANGED /jars/xmpcore (5.1.3 -> 5.1.2) VERSION_CHANGED /plugins/AnalyzeSkeleton_ (3.4.1 -> 3.3.0) VERSION_CHANGED /plugins/Stack_Manipulation (2.1.1 -> 2.1.2) VERSION_CHANGED /plugins/TrackMate_ (4.0.0 -> 5.2.0) VERSION_CHANGED /plugins/Trainable_Segmentation (3.2.29 -> 3.2.34) VERSION_CHANGED /plugins/Vaa3d_Writer (1.0.3 -> 1.0.2) VERSION_CHANGED /plugins/bUnwarpJ_ (2.6.11 -> 2.6.12) VERSION_CHANGED /plugins/bio-formats_plugins (6.3.0 -> 6.4.0) VERSION_CHANGED /plugins/register_virtual_stack_slices (3.0.5 -> 3.0.7) MOVED /jars/Correct_3D_Drift-1.0.3.jar -> /plugins/Correct_3D_Drift-1.0.3.jar MOVED /jars/KymographBuilder-2.1.1.jar -> /plugins/KymographBuilder-2.1.1.jar MOVED /jars/bigdataviewer_fiji-6.0.0.jar -> /plugins/bigdataviewer_fiji-6.0.0.jar MOVED /jars/ffmpeg-4.1-1.4.4-linux-x86_64.jar -> /jars/linux64/ffmpeg-4.1-1.4.4-linux-x86_64.jar MOVED /jars/metakit-5.3.2.jar -> /jars/bio-formats/metakit-5.3.2.jar MOVED /jars/ome-common-6.0.4.jar -> /jars/bio-formats/ome-common-6.0.4.jar MOVED /jars/ome-jai-0.1.0.jar -> /jars/bio-formats/ome-jai-0.1.0.jar MOVED /jars/ome-mdbtools-5.3.2.jar -> /jars/bio-formats/ome-mdbtools-5.3.2.jar MOVED /jars/ome-poi-5.3.3.jar -> /jars/bio-formats/ome-poi-5.3.3.jar MOVED /jars/ome-xml-6.0.1.jar -> /jars/bio-formats/ome-xml-6.0.1.jar MOVED /jars/specification-6.0.1.jar -> /jars/bio-formats/specification-6.0.1.jar ```

I added the class to this branch for now and will track my progress here if I make any, I don't think this branch will necessarily ever be merged, but it might produce separate PRs fixing individual issues.

[ctrueden]

I tried a couple of command line comparison tools but nothing was super helpful or colored.

How about this:

(cd Fiji.app && find .) | sort > app.txt
(cd Fiji.build && find .) | sort > build.txt
git diff --no-index --word-diff --word-diff-regex='[^/-]+' app.txt build.txt

[ctrueden]

For what it's worth—as I am working on improving this functionality this week—I pushed a script for diffing directories: ctrueden/ctr-scripts@452a6b5d7c90d9243af9497af7af495b62e17320. Useful for comparing two Fiji installations.

[ctrueden]

With scijava-maven-plugin 2.0.0, the copy-jars was renamed to populate-app. This renamed goal is now intended for either modifying an existing SciJava application (e.g. ImageJ or Fiji) environment, or building one from scratch, although it currently still falls short of this intent (see #17). But at least the naming is sensible now, and the bugs relating to native classifier JARs have been squashed!

[ctrueden]

I'm going to close this PR, since the populate-app exists and is the direction we want to take this. We may still want to add a feature where it downloads a JDK as part of the environment construction... but maybe not. Will revisit this later as needs arise.