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Bug 801 - Some plugins do not appear in subfolder but under plugins directly
Some plugins do not appear in subfolder but under plugins directly
Status: ASSIGNED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: Johannes Schindelin
Depends on:
Blocks:
 
Reported: 2014-06-19 13:25 CDT by Jan Brocher
Modified: 2014-06-23 15:28 CDT
4 users (show)

See Also:
Description Jan Brocher 2014-06-19 13:25:02 CDT 
In the most recent updated version of Fiji/IJ 2.0.0-rc5 some specific plugins do appear directly in the plugins loder even though they are located in a subfolder thereof. 
Those are for example: JACoP (which in my case is located in a folder named Colocalization) or for the manual "Cell Counter" plugin (in my case located in a folder named "Analyze"

Other plugins like self-written ones are displayed in the correct subfolder menu point.

cheers,
Jan

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140618215931)
Fiji: http://fiji.sc/update/ (last check:20140618220039)

Files not up-to-date:
  52941f0a (LOCAL_ONLY) 20120724120027 images/ToolIcon.png
  03fce6da (LOCAL_ONLY) 20120706180550 images/icon (BioVoxxel).png
  ff3d290a (LOCAL_ONLY) 20110307142230 images/icon (normal).png
  c30b7a18 (LOCAL_ONLY) 20140615103103 images/icon - Kopie.png
  8baeb36c (MODIFIED) 20140615103103 images/icon.png
  4deb407f (LOCAL_ONLY) 20140413132328 luts/Difference Indicator.lut
  99298680 (MODIFIED) 20140430123629 macros/StartupMacros.fiji.ijm
  dbf50690 (LOCAL_ONLY) 20140612124305 macros/toolsets/BASF Toolbar.ijm
  51b2e57a (LOCAL_ONLY) 20140519180637 macros/toolsets/BioVoxxel_Toolbox.ijm
  362707f5 (LOCAL_ONLY) 20140330181216 macros/toolsets/Filter_Menu.ijm
  1e2f8875 (LOCAL_ONLY) 20120903105628 macros/toolsets/Gamma Tool.txt
  febb9d05 (LOCAL_ONLY) 20131017152831 macros/toolsets/LineAndProfileTool.txt
  0f88195e (LOCAL_ONLY) 20140411114616 macros/toolsets/Montage Tools.ijm
  5e54fa1e (LOCAL_ONLY) 20130314141116 macros/toolsets/Multichannel and Stack Tools.txt
  545b95ef (LOCAL_ONLY) 20130528125840 macros/toolsets/Nearest_Neighbor_Indicator.ijm
  b6e9506b (LOCAL_ONLY) 20130314140737 macros/toolsets/ROI Manager Tools.txt
  e3fa44e3 (LOCAL_ONLY) 20140423214721 macros/toolsets/Stack Tools.ijm
  f6ae959f (LOCAL_ONLY) 20111029210608 macros/toolsets/Toolset Creator.txt
  3959d9a3 (LOCAL_ONLY) 20140430121549 macros/toolsets/Workshop_Menus.ijm
  8de3bfbb (LOCAL_ONLY) 20140124091116 plugins/ActionBar/BioVoxxel_bar.txt
  c8a057b9 (LOCAL_ONLY) 20140124092913 plugins/ActionBar/analysis_bar.txt
  5d7830e9 (LOCAL_ONLY) 20140124092115 plugins/ActionBar/filters_bar.txt
  44834401 (LOCAL_ONLY) 20121220144054 plugins/ActionBar/overlay_bar.txt
  ebe53ae9 (LOCAL_ONLY) 20140209142014 plugins/ActionBar/segmentation_bar.txt
  2f6a1b83 (LOCAL_ONLY) 20140124091527 plugins/ActionBar/selection_bar.txt
  13948d9d (LOCAL_ONLY) 20130721170100 plugins/ActionBar/test_bar.txt
  402a2633 (LOCAL_ONLY) 20140124091754 plugins/ActionBar/transformation_bar.txt
  52ff6766 (LOCAL_ONLY) 20130129192442 plugins/Analyze/Create_Template.jar
  3b647140 (LOCAL_ONLY) 20140501175454 plugins/Analyze/Find_Ridges.class
  11a9c570 (LOCAL_ONLY) 20140523171626 plugins/Analyze/MultipleKymograph_.class
  0c5c3f94 (LOCAL_ONLY) 20120718080724 plugins/Analyze/PCA/Compute.class
  b3fb8490 (LOCAL_ONLY) 20120718080724 plugins/Analyze/PCA/MSA_514.class
  29275003 (LOCAL_ONLY) 20120718080518 plugins/Analyze/Volumest_20101201.jar
  b2afde18 (LOCAL_ONLY) 20120612185532 plugins/Analyze/cell_counter.jar
  e281a3d7 (LOCAL_ONLY) 20140530103939 plugins/BASF/Analysis_Settings04.class
  054c4a86 (LOCAL_ONLY) 20140610220147 plugins/BASF/Threshold_Sections_v17.class
  1a93eb34 (LOCAL_ONLY) 20140320091532 plugins/Binary/Adjustable_Watershed.class
  bca18f7e (LOCAL_ONLY) 20140426234304 plugins/BioVoxxel/Adaptive_Filter02.class
  bb1bb5cf (LOCAL_ONLY) 20140505083440 plugins/BioVoxxel/Advanced_Particle_Analyzer.class
  1ddc6498 (LOCAL_ONLY) 20140505125519 plugins/BioVoxxel/Advanced_Particle_Analyzer02.class
  1b231415 (LOCAL_ONLY) 20140507172829 plugins/BioVoxxel/Advanced_Particle_Analyzer03.class
  833a8fcd (LOCAL_ONLY) 20140407203108 plugins/BioVoxxel/Advanced_Particle_Analyzer_Test.class
  4d93a69c (LOCAL_ONLY) 20140507221541 plugins/BioVoxxel/Extended_Particle_Analyzer.class
  bedbc713 (LOCAL_ONLY) 20140507230253 plugins/BioVoxxel/Extended_Particle_Analyzer_Test.class
  76cc0e1f (LOCAL_ONLY) 20140508110753 plugins/BioVoxxel/Extended_Particle_Analyzer_Test02.class
  4e0330a7 (LOCAL_ONLY) 20140508153949 plugins/BioVoxxel/Extended_Particle_Analyzer_Test03.class
  ca3b344e (LOCAL_ONLY) 20140508181916 plugins/BioVoxxel/Extended_Particle_Analyzer_Test04.class
  860a79c2 (LOCAL_ONLY) 20140509112400 plugins/BioVoxxel/Extended_Particle_Analyzer_Test05.class
  6ae1ff9d (LOCAL_ONLY) 20140509132248 plugins/BioVoxxel/Extended_Particle_Analyzer_Test06.class
  57735677 (LOCAL_ONLY) 20140512120325 plugins/BioVoxxel/Extended_Particle_Analyzer_Test07.class
  48205e75 (LOCAL_ONLY) 20140512190444 plugins/BioVoxxel/Extended_Particle_Analyzer_Test08.class
  be0de061 (LOCAL_ONLY) 20140427002226 plugins/BioVoxxel/Gaussian_Weighted_Median02.class
  954969d9 (LOCAL_ONLY) 20140514193714 plugins/BioVoxxel/Pseudo_flat_field_correction01.class
  ac2b9245 (LOCAL_ONLY) 20140515105243 plugins/BioVoxxel/Pseudo_flat_field_correction02.class
  bcd9cc13 (LOCAL_ONLY) 20140515220911 plugins/BioVoxxel/Pseudo_flat_field_correction03.class
  4b963e0f (LOCAL_ONLY) 20140516084911 plugins/BioVoxxel/Pseudo_flat_field_correction04.class
  484f2f1a (LOCAL_ONLY) 20140516140638 plugins/BioVoxxel/Pseudo_flat_field_correction05.class
  749f45a0 (LOCAL_ONLY) 20140331095117 plugins/Colocalization/Colocalization_Colormap_.jar
  71331805 (LOCAL_ONLY) 20120815173201 plugins/Colocalization/jacop_.jar
  925f2bdd (LOCAL_ONLY) 20120602170419 plugins/Color/Alpha_Channel.class
  aefd11ed (LOCAL_ONLY) 20130315165456 plugins/Color/Color_Transformer.class
  e2d6a637 (LOCAL_ONLY) 20140209104729 plugins/Color/Color_Transformer_2.class
  dcea879b (LOCAL_ONLY) 20131208134611 plugins/Deconvolution/Diffraction_PSF_3D.class
  af22a2df (LOCAL_ONLY) 20131208134607 plugins/Deconvolution/Iterative_Deconvolve_3D.class
  8d9bdfa0 (LOCAL_ONLY) 20090703152912 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  c8a61322 (LOCAL_ONLY) 20140430130459 plugins/Droplet_.jar
  03999f43 (LOCAL_ONLY) 20110711135856 plugins/EDF/Demo.class
  2b08ff32 (LOCAL_ONLY) 20110711140036 plugins/EDF/EDF-demo.txt
  df409258 (LOCAL_ONLY) 20110711140720 plugins/EDF/EDF_Easy_.class
  97036c5b (LOCAL_ONLY) 20110711135856 plugins/EDF/EDF_Expert_.class
  26eaeb16 (LOCAL_ONLY) 20110711135856 plugins/EDF/EDF_Viewer3D_.class
  3f5cc128 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/AbstractEdfAlgorithm.class
  94cb75b0 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/Color2BW.class
  8e6be0b2 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/EdfComplexWavelets.class
  fb218014 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/EdfRealWavelets.class
  a7ef1a84 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/EdfSobel.class
  92c9b291 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/EdfVariance.class
  6916bcdd (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/EdfWaveletMaximumModulus.class
  9fbcfcd1 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/LogSingleton.class
  267fe2fc (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/MorphologicalOperators.class
  ed732583 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/PostProcessing.class
  ed51b555 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/ProcessTopology.class
  2321c8d8 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/Sobel.class
  bb9ae47e (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/Tools.class
  2b8ba320 (LOCAL_ONLY) 20110711135856 plugins/EDF/edf/Variance.class
  1aedfb3f (LOCAL_ONLY) 20110711163530 plugins/EDF/edfgui/AboutDialog.class
  0c639c6c (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/AbstractDialog$TimerListener.class
  f2c07124 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/AbstractDialog.class
  7ed319d6 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/AdvancedDialog$MyVerifier.class
  d488e269 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/AdvancedDialog.class
  7be3ea66 (LOCAL_ONLY) 20110711163612 plugins/EDF/edfgui/BasicDialog.class
  e88712ba (LOCAL_ONLY) 20110711140956 plugins/EDF/edfgui/ExtendedDepthOfField.class
  5ca9e395 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/LogPane.class
  f0f56b51 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/MySlider.class
  442538e1 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/MyTableRenderer.class
  265b3bea (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/Parameters.class
  6ec6b0e1 (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/SimpleTableModel.class
  a404eb8e (LOCAL_ONLY) 20110711140924 plugins/EDF/edfgui/ThreadEdf.class
  db8163fa (LOCAL_ONLY) 20110711135856 plugins/EDF/edfgui/ThreadTopoProc.class
  b77b5da8 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Access.class
  895118eb (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Buffer.class
  8f404b54 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Builder.class
  0caa808d (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ByteAccess.class
  f773aa9e (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ByteBuffer.class
  d31572ce (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/BytePointwise.class
  a1c28f6c (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ByteProcess.class
  f91ef099 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ByteSet.class
  10ade4a4 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Convolver.class
  79469ee7 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Display.class
  c1576be6 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/DoubleAccess.class
  3bb456d7 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/DoubleBuffer.class
  eed062ce (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/DoublePointwise.class
  e3f707cd (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/DoubleProcess.class
  f7d47d5d (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/DoubleSet.class
  3c98dbe0 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FMath.class
  e72c54a9 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FloatAccess.class
  752ca783 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FloatBuffer.class
  13d2c8ed (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FloatPointwise.class
  f92fc306 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FloatProcess.class
  cbb54e2a (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/FloatSet.class
  a4b3f20a (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ImageAccess.class
  a3cb9815 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ImageWare.class
  3b5db209 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Pointwise.class
  bab794cb (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/Process.class
  2475b92b (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ShortAccess.class
  589b6994 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ShortBuffer.class
  808d9fc0 (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ShortPointwise.class
  7a16250c (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ShortProcess.class
  9edb2a7c (LOCAL_ONLY) 20110711140036 plugins/EDF/imageware/ShortSet.class
  2cecb7c4 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$1.class
  d701e2d7 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$2.class
  aa71cdde (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Cube.class
  75f963eb (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$CustomWindow$1.class
  9f71ceeb (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$CustomWindow.class
  be688c54 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$ImageRegion.class
  3370662a (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Lines.class
  8ae02fcd (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Lut.class
  c1648126 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Misc.class
  9919bf14 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Picture.class
  16ac3c3a (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$PlotVal.class
  d717fe7c (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$TextField.class
  f954757f (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D$Transform.class
  fb38ada4 (LOCAL_ONLY) 20110711135856 plugins/EDF/surfacemap/SurfaceMap3D.class
  6d6af260 (LOCAL_ONLY) 20110711140036 plugins/EDF/wavelets/ComplexWaveFilter.class
  62046e79 (LOCAL_ONLY) 20110711140036 plugins/EDF/wavelets/ComplexWavelet.class
  b3f1dbba (LOCAL_ONLY) 20110711140036 plugins/EDF/wavelets/ImageAccess.class
  68788aa5 (LOCAL_ONLY) 20110711140036 plugins/EDF/wavelets/WaveSpline.class
  f469ca9f (LOCAL_ONLY) 20110711140036 plugins/EDF/wavelets/WaveSplineFilter.class
  e6545de9 (LOCAL_ONLY) 20140527192022 plugins/FigureJ_.jar
  0fb65ed4 (LOCAL_ONLY) 20140430131709 plugins/Filters/Adaptive_Filter.class
  f02e6e81 (LOCAL_ONLY) 20130624145025 plugins/Filters/Edge_Enhancement.ijm
  7f2acd01 (LOCAL_ONLY) 20140422155505 plugins/Filters/Enhance_True_Color_Contrast.class
  448b2287 (LOCAL_ONLY) 20140408084334 plugins/Filters/Gaussian_Weighted_Median.class
  9bdfcd0a (LOCAL_ONLY) 20130813164727 plugins/Filters/Hybrid_2D_Median_Filter.class
  2c9ade75 (LOCAL_ONLY) 20140505091915 plugins/Filters/Limited_Mean.class
  61d742a8 (LOCAL_ONLY) 20140224094701 plugins/Filters/Lipschitz_.class
  328fe563 (LOCAL_ONLY) 20131128112022 plugins/Filters/Manual_Threshold_Quant.ijm
  e255711a (LOCAL_ONLY) 20140223204214 plugins/Filters/Mean_Shift.class
  ee9b1292 (LOCAL_ONLY) 20121119175722 plugins/Filters/Mexican_Hat_Filter.class
  1656d24d (LOCAL_ONLY) 20140516141441 plugins/Filters/Pseudo_flat_field_correction.class
  adbd06cc (LOCAL_ONLY) 20130624144145 plugins/Filters/Thresholded_Blur.class
  85f658a2 (LOCAL_ONLY) 20140430130459 plugins/IJ_Ed2.jar
  ad9dcb27 (MODIFIED) 20140430130459 plugins/LSM_Reader.jar
  b97c3a95 (LOCAL_ONLY) 20120807122350 plugins/Macros/3D Cluster Analysis.txt
  ecb420cd (LOCAL_ONLY) 20130722114723 plugins/Macros/Image_to_Icon.txt
  d84cc2bb (LOCAL_ONLY) 20100922214634 plugins/Morphology/Add_Borders.class
  5cccefae (LOCAL_ONLY) 20100913095428 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20100913095434 plugins/Morphology/AnnularDilation.txt
  5d777e5e (LOCAL_ONLY) 20100928170030 plugins/Morphology/BinaryConditionalDilate_.class
  6cfae168 (LOCAL_ONLY) 20060525192652 plugins/Morphology/BinaryConditionalErode_.class
  877be8e6 (LOCAL_ONLY) 20060525192958 plugins/Morphology/BinaryConnectivity_.class
  ebe4d9b0 (LOCAL_ONLY) 20111110085448 plugins/Morphology/BinaryDilateNoMerge4_.class
  65b35fcd (LOCAL_ONLY) 20111109155612 plugins/Morphology/BinaryDilateNoMerge8_.class
  da5dc033 (LOCAL_ONLY) 20081019152450 plugins/Morphology/BinaryDilateTest.txt
  fe9208a2 (LOCAL_ONLY) 20060525193012 plugins/Morphology/BinaryDilate_.class
  9f2b4ef9 (LOCAL_ONLY) 20081019152918 plugins/Morphology/BinaryErodeTest.txt
  b38e2aa0 (LOCAL_ONLY) 20060525193102 plugins/Morphology/BinaryErode_.class
  3f39caaf (LOCAL_ONLY) 20060525101716 plugins/Morphology/BinaryFilterReconstruct.txt
  76eb6799 (LOCAL_ONLY) 20090525193222 plugins/Morphology/BinaryFilterReconstruct_.class
  6a2c8b7a (LOCAL_ONLY) 20111109154430 plugins/Morphology/BinaryGeodesicDilateNoMerge8_.class
  14c67860 (LOCAL_ONLY) 20080602091844 plugins/Morphology/BinaryHitOrMiss_.class
  33b507c2 (LOCAL_ONLY) 20100418152848 plugins/Morphology/BinaryKillBorders_.class
  134d68cd (LOCAL_ONLY) 20140205190552 plugins/Morphology/BinaryLabel8_.class
  d3c84f8c (LOCAL_ONLY) 20070712112240 plugins/Morphology/BinaryLabelMacro.txt
  59e1afe9 (LOCAL_ONLY) 20100508085308 plugins/Morphology/BinaryLabel_.class
  36e4a042 (LOCAL_ONLY) 20060525101718 plugins/Morphology/BinaryPrune.txt
  c8c66f92 (LOCAL_ONLY) 20090526165400 plugins/Morphology/BinaryReconstruct_.class
  3ff298c7 (LOCAL_ONLY) 20060525193502 plugins/Morphology/BinaryThick2_.class
  b73f68f4 (LOCAL_ONLY) 20060525193450 plugins/Morphology/BinaryThick_.class
  2c4c813e (LOCAL_ONLY) 20060525193520 plugins/Morphology/BinaryThin2_.class
  d8a5d664 (LOCAL_ONLY) 20060525193512 plugins/Morphology/BinaryThin_.class
  3e83cc61 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary8_.txt
  e9fc745d (LOCAL_ONLY) 20090602153322 plugins/Morphology/Catalogue_Particles.txt
  4d0095a2 (LOCAL_ONLY) 20070607090848 plugins/Morphology/Classify_Particles.class
  f53a898e (LOCAL_ONLY) 20090511083446 plugins/Morphology/CloseByReconstructionTopHat.txt
  2c7f38f5 (LOCAL_ONLY) 20101005103840 plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20060525101718 plugins/Morphology/Corners.txt
  55c709bf (LOCAL_ONLY) 20061116092256 plugins/Morphology/Correlate_Results.class
  d463ee86 (LOCAL_ONLY) 20081019163010 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Diagonal8to4.txt
  61193e21 (LOCAL_ONLY) 20100929125932 plugins/Morphology/Domes_.class
  e428a0f5 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Domes_stack.txt
  1be944ae (LOCAL_ONLY) 20090506082436 plugins/Morphology/DoubleWaterfall.txt
  925d3d8c (LOCAL_ONLY) 20111208091210 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20111208091158 plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20111208091142 plugins/Morphology/DrawConvexHulls.txt
  d9ae9295 (LOCAL_ONLY) 20111208091226 plugins/Morphology/DrawFeret_Breadth.txt
  f1a7575d (LOCAL_ONLY) 20111208091236 plugins/Morphology/DrawMinR_MaxR.txt
  288ace7a (LOCAL_ONLY) 20100805124116 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20081019170232 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Minima.txt
  2b80b381 (LOCAL_ONLY) 20100418175426 plugins/Morphology/FillHolesReconstruct.txt
  205b6052 (LOCAL_ONLY) 20060525130102 plugins/Morphology/Fill_Border_Holes.txt
  54d7ef21 (LOCAL_ONLY) 20090506082436 plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20101001143722 plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  6f716dcc (LOCAL_ONLY) 20101001143322 plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20090504142458 plugins/Morphology/GreyscaleCentreFilter.txt
  c4267b67 (LOCAL_ONLY) 20060525193602 plugins/Morphology/GreyscaleDilate_.class
  d8091e12 (LOCAL_ONLY) 20131021105343 plugins/Morphology/GreyscaleErode_.class
  0a50379d (LOCAL_ONLY) 20100920132950 plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20090503182436 plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20090504122820 plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20090504123000 plugins/Morphology/GreyscaleProperOpen.txt
  9aadbae0 (LOCAL_ONLY) 20090526165732 plugins/Morphology/GreyscaleReconstruct_.class
  4d7e6035 (LOCAL_ONLY) 20100908144402 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20100908144826 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20060525101718 plugins/Morphology/H-break.txt
  a73d2279 (LOCAL_ONLY) 20090511130552 plugins/Morphology/HMaxima_Transform.txt
  f1c1b630 (LOCAL_ONLY) 20090527092132 plugins/Morphology/HMinima_Transform.txt
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Comment 1 Jan Brocher 2014-06-19 13:39:49 CDT 
Additionally, the Refresh Menu option is blocked in the "Help" menu.
Comment 2 Johannes Schindelin 2014-06-19 21:09:59 CDT 
Yes, Help>Refresh Menus is disabled for now. It is just too hard to support it properly. I hope to be able to resurrect it, but for now, we simply cannot support it. Sorry!

As to the .jar files in subdirectories: wow. What a "magical" feature. Even I did not know about it, and TBH I find it highly unintuitive.

However, I vowed to pursue backwards compatibility, so I will address this issue soon, hopefully tomorrow, but certainly until end of next week!
Comment 3 Johannes Schindelin 2014-06-20 10:58:11 CDT 
Jan replied:

> Hi Johannes,
>
> First of all, this might anyway be a very minor issue in comparison to all
> the things you and all the colleagues need to think about now.
> Second, if this "unintuitive" behaviour is not intented, i guess we (at
> least I) can live with it, if jar files in future are never shown in the
> respective subdirectories but only *.class files.
> I am also not asking for a detailed explanation for the unintuitiveness
>  (to save you time) since it might be obvious and unintuitive to many and
> as mentioned it is actually a minor issue.
>
> Anyway, since you and all the IJ2 team is mostly bombarded with mails about
> thinks which are not working, I wanted to congratulate you and say thanks
> for the big effort and all the thousands of thing which are working
> undetected by the users already now, considering such a big change.
>
> All of you are doing really a great work and I feel a little embarrassed
> not being able to contribute more than only sending annoying questions or
> bug reports (even though that might be important).
>
> kind regards,
> Jan

First of all: thank you for your kind words. You have no idea how big a difference they make.

Second: I am serious about backwards compatibility. I know that ImageJ 1.x breaks backwards compatibility with itself quite often, and I cannot do anything about that. At least not much. But I can do something about backwards compatibility of Fiji/ImageJ2 and I will try very hard to keep it.

So I will address the issue you reported, hopefully soon (to add insult to injury, this morning we found all of our servers rebooted, some services having problems, one server even not rebooting on its own, and the server offering the Fiji Wiki getting stuck on something or else, therefore we're even more swamped today than we already are).

And thank you for your patience with reporting bugs and being helpful!
Comment 4 Curtis Rueden 2014-06-23 15:28:37 CDT 
Assigning to Johannes, who plans to address this as time allows.