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fiji/fiji-linux64/Fiji.app/README.md

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-[![](https://github.com/fiji/fiji/actions/workflows/build-main.yml/badge.svg)](https://github.com/fiji/fiji/actions/workflows/build-main.yml)
-[![developer chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://imagesc.zulipchat.com/#narrow/stream/327238-Fiji)
-[![Image.sc Forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Ffiji.json&query=%24.topic_list.tags.0.topic_count&colorB=green&&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/fiji)
-
-[ Fiji Is Just ImageJ ]
-=======================
-
-Fiji is a "batteries-included" distribution of
-[ImageJ](http://imagej.net/)—a popular, free scientific image processing
-application—which includes a lot of plugins organized into a coherent
-menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
-
-The main focus of Fiji is to assist research in life sciences.
-
-At the moment, the following platforms are supported:
-
-- Windows Intel 32-bit/64-bit
-- Linux Intel 32-bit/64-bit
-- MacOSX Intel 32-bit/64-bit (partial support for PowerPC 32-bit)
-- all platforms supporting Java and a POSIX shell, via `bin/ImageJ.sh`
-
-The setup is as easy as unpacking the portable archive and
-double-clicking the [ImageJ
-launcher](https://github.com/imagej/imagej-launcher).
-
-Fiji is intended to be the most painless, easy, quick and convenient way
-to install ImageJ and plugins and keep everything up-to-date.
-
-
-Usage
------
-
-Fiji is meant to be distributed without source, to make the download as
-small as possible. In the basic version, Fiji is a portable application,
-i.e. it should run wherever you copy it.
-
-The starting point is the ImageJ launcher, which will launch Java, set
-up the environment, and call ImageJ.
-
-To pass arguments to ImageJ, just specify them on the command line.
-
-To pass arguments to the Java Virtual Machine, specify them on the
-command line, separating them from the ImageJ arguments (if any) with a
-`--`.  In other words, if you want to override the memory setting, call
-Fiji like this:
-
-	$ ./ImageJ-linux32 -Xmx128m --
-
-Open Source
------------
-
-We are dedicated to open source. Not only does open source allow other
-developers to port the application to new platforms that the original
-authors did not begin to think of, it allows scientists to study the
-code to understand the inner workings of the algorithms used, and it
-permits others to use the program in totally new ways, and enhance it in
-all imaginable ways.
-
-Therefore, the majority of Fiji is licensed under the GNU Public License
-version 2. Exceptions are listed in the
-[LICENSES](https://github.com/fiji/fiji/blob/master/LICENSES) file.
-
-Fiji's source code is split up into a [main
-repository](https://github.com/fiji/fiji), containing the top-level project and
-support scripts, while all components live in their own repositories in the
-[Fiji organization on GitHub](https://github.com/fiji/). As a rule of thumb: the
-file name and the project name correspond pretty well, e.g. fiji-lib.jar is
-maintained in [fiji-lib](https://github.com/fiji/fiji-lib).
-
-Participating
--------------
-
-[Pull Requests](https://help.github.com/articles/using-pull-requests)
-are very welcome!
-
-See the [Contributing](http://imagej.net/Contributing) page of the ImageJ wiki.
-
-Authors
--------
-
-* Fiji was created by
-  [Johannes Schindelin](https://imagej.net/User:Schindelin).
-  It is currently maintained by [Curtis Rueden](https://imagej.net/User:Rueden)
-  of [LOCI](https://imagej.net/LOCI) at the University of Wisconsin-Madison.
-* ImageJ 1.x was created and is maintained by
-  [Wayne Rasband](https://imagej.net/Wayne_Rasband).
-* ImageJ2 was created and is maintained by Curtis Rueden.
-* For a list of most recent contributors, please refer to the
-  [Contributors](http://imagej.net/Contributors) page of the ImageJ wiki.
-
-Thanks
-------
-
-We are very grateful to Wayne Rasband, who is not only a very dedicated
-developer of ImageJ 1.x; he also fosters an active and friendly
-community around ImageJ.
-
-We are especially grateful to be part of an outstanding
-[community](http://imagej.net/Community) who is active, friendly and
-helping to scientists understanding and analysing images every day.
-
-Oh, and Fiji is also an island. We just wanted to let you know.

fiji/fiji-linux64/Fiji.app/WELCOME.md

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-# Welcome to Fiji
-
-[Fiji](https://fiji.sc/) is a package for scientific
-image analysis—a "batteries-included" distribution of
-[ImageJ](https://imagej.net/software/imagej) with many plugins.
-
-Please report problems either [on the Image.sc Forum](https://forum.image.sc/)
-("New Topic" button, "Usage & Issues" category, `fiji` tag) or
-[on GitHub](https://github.com/fiji/fiji/issues/new).
-
-Best wishes for successful image analysis, and we hope Fiji is helpful to you!

fiji/fiji-linux64/Fiji.app/config/jaunch/common.toml

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-# ==============================================================================
-# *** Welcome to Jaunch's base configuration file! ***
-# ==============================================================================
-#
-# Jaunch is a native binary (two per platform, actually) to discover non-native
-# runtimes including Python and the Java Virtual Machine (JVM), start them, and
-# run programs using them. Via its TOML-based configuration mechanism, Jaunch
-# is designed to be powerful and flexible without the need to edit or recompile
-# the Jaunch source code.
-#
-# This common.toml file contains useful general-purpose, non-application-specific
-# configuration that defines some sensible defaults for typical launchers.
-# You can of course edit it to customize Jaunch's behavior however you like.
-#
-# Each application will have its own extensions to the general configuration
-# defined in another TOML file named the same as its native launcher executable.
-# For example, if you have a native executable named fizzbuzz for launching your
-# FizzBuzz application, you would also write a fizzbuzz.toml companion file that
-# overrides or augments this configuration with fizzbuzz-specific settings.
-#
-# Alternately, if you would like to keep all configuration together in one file
-# for simplicity, you can write a single TOML file with everything, and name it
-# either `jaunch.toml` or the same as your native launcher (e.g. `fizzbuzz.toml`).
-#
-# For simple and concrete demo application examples, see doc/EXAMPLES.md.
-#
-# Without further ado, let's dive into the configuration!
-
-# ==============================================================================
-# jaunch-version
-# ==============================================================================
-# The version of Jaunch with which this configuration file is intended to work.
-# Leave this value be, unless you are upgrading from an older version of Jaunch.
-
-jaunch-version = 1
-
-# ==============================================================================
-# program-name
-# ==============================================================================
-# The name of your program! This name will appear in usage text and dialog boxes.
-
-#program-name = 'FizzBuzz'
-
-# ==============================================================================
-# includes
-# ==============================================================================
-# Other configuration files to recursively combine with this one.
-# This mechanism can help to better organize your configuration logic.
-# Or turn it into a gigantic mess, if you enjoy overengineered spaghetti.
-
-includes = []
-
-# ==============================================================================
-# supported-options
-# ==============================================================================
-# The list of command line options supported by Jaunch out of the box.
-#
-# These are arguments that Jaunch will interpret, transforming them in various ways
-# into arguments to the main program that is launched, and/or the runtime itself.
-#
-# The syntax here is hopefully self-explanatory by reading through the list.
-# But here are the technical details anyway just in case:
-#
-# * The pipe symbol (|) divides the declaration of the option itself from its help text.
-#   The help text is not required, but recommended, and will be shown when Jaunch's help
-#   directive is invoked (which happens out of the box when the --help option is given).
-#
-# * Options may be standalone (like --debug), or may take a parameter.
-#
-# * To declare an option as requiring a parameter, simply write an equals sign
-#   (=) after the option flag. What you write after the equals sign does not
-#   matter, except that it will be shown that way in the help text.
-#
-# * Jaunch parses parameters given as either a single argument --count=123 with an
-#   equals sign (=), or as two arguments (--count 123) separated by a space.
-#
-# * The parameter value given by the user will be stored into Jaunch's variables
-#   using the canonical name of the option in question. So for example,
-#   --count=456 will store the value "456" into the variable called count.
-#   Variables can be used within strings using `${...}` syntax, e.g. `${count}`.
-#   Jaunch also recognizes system environment variables, so you can use
-#   expressions like e.g. `${PATH}` if you like as well.
-#
-# * Options may have any number of aliases, separated by commas. So e.g.
-#   --size,length=<number> would let both --size=37 and --length=37 work,
-#   storing the value "37" into the variable called "size" since it comes first.
-#
-# * If you need to use an actual pipe symbol (|) as part of your option or help text, you
-#   can't, sorry! It's not a good idea anyway, because that symbol is used by shells to
-#   indicate I/O piping between processes. So making it part of an option would be super
-#   tricky and confusing. That's why Jaunch uses the pipe symbol as its separator:
-#   because it is very unlikely to be needed as an actual character anywhere.
-#
-# See python.toml and jvm.toml for more supported-options examples.
-
-supported-options = [
-    '--help,-h|show this help',
-    '--dry-run|show the command line, but do not run anything',
-    '--debug|verbose output',
-    '--headless|run in text mode (without any GUI)',
-    '--print-app-dir|print directory where the application is located',
-    '--print-config-dir|print directory where the configuration files are located',
-    '--system|do not try to run bundled runtime',
-]
-
-# ==============================================================================
-# os-aliases, arch-aliases
-# ==============================================================================
-# Aliases for operating system names and CPU architectures, respectively.
-# Used when analyzing root directory names.
-
-os-aliases = [
-    "LINUX:linux",
-    "MACOSX:darwin,macos,macosx",
-    "WINDOWS:win,windows",
-    "IOS:ios",
-    "ANDROID:android",
-]
-arch-aliases = [
-    "ARM32:aarch32,arm32",
-    "ARM64:aarch64,arm64",
-    "X86:i386,i486,i586,i686,x86-32,x86_32,x86",
-    "X64:amd64,x86-64,x86_64,x64",
-]
-
-# ==============================================================================
-# modes
-# ==============================================================================
-# List of additional hints to enable or disable based on other hints.
-#
-# ------------------------------------------------------------------------------
-# Before we talk about modes, though, we need to explain what hints are.
-#
-# In many of Jaunch's sections, each string element may be prefixed with one or
-# more segments separated by pipes. Each such segment is a *hint* for Jaunch
-# regarding a flag that must be set for that particular line to be considered.
-# A hint prefixed by a bang symbol (!) negates the hint, making that segment
-# match only when that particular hint is *not* set.
-#
-# Here is an example:
-#     '!--quiet|OS:LINUX|ARCH:X64|-Dmessage=Linuuuux-64-BITS!',
-#
-# Above, the string '-Dmessage=Linuuuux-64-BITS!' will be included in
-# the list if and only if the hints OS:LINUX and ARCH:X64 are set, and
-# the --quiet hint is NOT set (since it is negated with the bang symbol).
-#
-# Jaunch sets hint flags based on a few sources:
-#
-# * Active operating system: OS:LINUX, OS:MACOSX, OS:WINDOWS,
-#   OS:IOS, OS:ANDROID, OS:WASM, OS:TVOS, OS:WATCHOS, or OS:UNKNOWN.
-#
-# * Active CPU architecture: ARCH:ARM32, ARCH:ARM64, ARCH:X86, ARCH:X64,
-#   ARCH:MIPS32, ARCH:MIPSEL32, ARCH:WASM32, or ARCH:UNKNOWN.
-#
-# * Option hints, set from arguments passed to Jaunch, each of which sets a matching
-#   hint. For example, passing the --system option will set a hint '--system'.
-#
-# * Mode hints, set from evaluation of the modes field (we're getting there!).
-#
-# * Runtime-specific hints, based on the runtime installation(s) selected.
-#   For example:
-#
-#   - PYTHON:3.9 if the selected Python installation is version 3.9.
-#   - PYTHON:3.9+ if the selected Python installation is version 3.9 or later.
-#   - JAVA:9 if the selected Java installation is version 9.
-#   - JAVA:9+ if the selected Java installation is version 9 or later.
-#   - and so on.
-#
-#   Of course, runtime hints will only be set after matching an installation.
-#   For more details about runtime hints, see the root-paths documentation in
-#   runtime-specific configuration files python.toml and jvm.toml.
-#
-# ------------------------------------------------------------------------------
-# Now that we understand hints: what is this modes section all about?
-#
-# With modes, you can set (or unset) a single hint in response to different other
-# hints, which can help to consolidate rules in other sections of the configuration.
-# Modes can also be used to negate hints. It's easiest to explain via an example.
-#
-# Suppose your program wants to support the following three options:
-#
-# * --headless, which enables headless mode, disabling the GUI.
-# * --batch, which enables a mode to run sequential computations.
-# * --big-gui, to use the *BIG* GUI, when you like it large!
-#
-# Let's say that use of the batch mode implies headless operation,
-# while use of the big GUI is incompatible with headless.
-#
-# You might define the following modes here:
-#
-#     '--headless|headless',
-#     '--batch|headless',
-#     '--big-gui|!headless',
-#
-# In this way, whenever either --headless or --batch is passed, the headless mode hint
-# will be enabled, and whenever --big-gui is passed, the headless mode is disabled.
-# If multiple conflicting arguments are passed, the ultimate state of headless mode will
-# depend on the order of such arguments, since mode lines are evaluated sequentially.
-#
-# The main advantage of this extra layer of indirection is that configuration elsewhere
-# in the TOML file based on whether headless mode is active can simply use the single
-# unified headless hint, rather than needing to recapitulate all the (possibly evolving
-# over time) special cases in multiple places, improving config clarity and maintenance.
-
-modes = []
-
-# ==============================================================================
-# directives
-# ==============================================================================
-# Commands that define what actually happens during launch.
-#
-# Each one runs at a particular (hardcoded) time during configuration.
-# Directives unsupported by the configurator program are ignored.
-#
-# This may seem confusingly abstract, but the basic idea is this: maybe you want
-# Jaunch *not* to launch the usual program this time, but rather to do something else!
-#
-# What sorts of other things? you might ask. And how can we possibly define
-# such open-ended behavior in a mere TOML configuration file? Well, the short
-# answer is: we can't. The configurator program that ships with Jaunch has some
-# built-in directives, and that's it. As of this writing, those are:
-#
-# * ABORT              - Cancel the launch without displaying an error message.
-# * ERROR              - Cancel the launch and display an error message to the user.
-#
-# * help               - Display the usage text, built from the supported-options above.
-# * dry-run            - Display the final launch command with runtime args + main args.
-#                        Useful to see what would happen, without it actually happening.
-# * print-app-dir      - Print out the path to the application. Typically, this will be
-#                        the folder containing the launcher.
-# * print-config-dir   - Print out the path to the configuration directory.
-#
-# Directives in UPPER CASE are native launch modes handled on the C/native side,
-# while directives in web-case are executed on the configurator side.
-#
-# Some additional directives are runtime-specific; see the directives documentation
-# in runtime-specific configuration files python.toml and jvm.toml.
-#
-# If you need to support other directives besides those above, you'll have to
-# hack the Kotlin and/or C source code, and also write rules here in the TOML.
-#
-# But if you simply want to disable e.g. Jaunch's built-in help, you can safely
-# remove the `--help` and `-h` lines below to do so.
-
-directives = [
-  '--dry-run|dry-run,ABORT',  # <-- Order matters! Turn on dry-run mode right away.
-  '--help|help,ABORT',
-  '-h|help,ABORT',
-  '--print-app-dir|print-app-dir',
-  '--print-config-dir|print-config-dir',
-]
-
-# ==============================================================================
-# allow-unrecognized-args
-# ==============================================================================
-# Whether to allow unrecognized arguments to be passed to the runtime.
-#
-# When the minus-minus (--) divider is absent, the only args that end up as
-# runtime args will be ones from the runtime-specific `recognized-args` lists
-# (see python.toml and jvm.toml for examples). But if the minus-minus divider
-# *is* given, it becomes possible to force a particular argument to be construed
-# as an argument to the runtime, even when it does not appear on the list.
-#
-# For example, suppose for a JVM-based application called JFizzBuzz the user writes:
-#
-#     ./jfb -ZZ:SuperSecretOption -- 1 2 3 4 5
-#
-# Using the config in jvm.toml, Jaunch would translate this into something like:
-#
-#     .../bin/java -ZZ:SuperSecretOption org.fizzbuzz.FizzBuzz 1 2 3 4 5
-#
-# However, depending on your application, it might not be desirable for
-# such unrecognized args to be allowed through to the program launch.
-#
-# * If you want to allow all user-specified runtime args through to the
-#   program launch, even when they aren't recognized, set this value to true.
-#
-# * If you want full control over what arguments the user can pass to the runtime,
-#   set this value to false, and edit the appropriate recognized-args list
-#   according to your needs. Then Jaunch will fail fast when told to pass an
-#   unrecognized option to the runtime.
-#
-# If you know Java, you probably know that it will barf when confronted with an
-# argument like -ZZ:SuperSecretOption. But maybe you are using a custom build of
-# OpenJDK produced by your organization's new superintelligent AI, which
-# actually *does* have this option! Who is Jaunch to judge? (In that case, I
-# would argue you should really just add '-ZZ:*' to the `jvm.recognized-args`
-# list in jvm.toml, but then I would be judging.) Or maybe you just want to
-# trust your users as OpenJDK evolves, rather than dealing with the bureaucracy
-# of updating the TOML file every time OpenJDK changes its supported options.
-# In such cases, this option is here for you.
-
-allow-unrecognized-args = false
-
-# You did it! It's the end. :clap: Bye now.

fiji/fiji-linux64/Fiji.app/config/jaunch/fiji.py

@@ -1,90 +0,0 @@
-import os
-import sys
-
-import imagej
-import scyjava
-
-from pathlib import Path
-
-
-# Credit: https://stackoverflow.com/a/640431/1207769
-from ctypes import POINTER, c_int, cast, pythonapi
-def in_interactive_inspect_mode():
-    """Whether '-i' option is present or PYTHONINSPECT is not empty."""
-    if os.environ.get('PYTHONINSPECT'): return True
-    iflag_ptr = cast(pythonapi.Py_InteractiveFlag, POINTER(c_int))
-    #NOTE: in Python 2.6+ ctypes.pythonapi.Py_InspectFlag > 0
-    #      when PYTHONINSPECT set or '-i' is present
-    return iflag_ptr.contents.value != 0
-
-
-def launch_fiji():
-    # Discern app directory.
-    app_dir = Path(__file__).parent
-
-    # Find the divider argument.
-    divider = "--"
-    try:
-        div_index = sys.argv.index(divider)
-    except AttributeError:
-        div_index = -1
-
-    # Validate argument syntax.
-    if len(sys.argv) < 4 or div_index < 0 or div_index > len(sys.argv) - 2:
-        print(
-            "Usage: fiji.py path-to-libjvm [jvm-arg1 ... jvm-argN] "
-            f"{divider} main-class [main-arg1 ... main-argN]"
-        )
-        sys.exit(1)
-
-    # Parse out the arguments.
-    libjvm_path = sys.argv[1]
-    jvm_args = sys.argv[2:div_index]
-    main_class = sys.argv[div_index+1]
-    main_args = sys.argv[div_index+2:]
-
-    # Isolate any classpath arguments.
-    classpath_prefix = "-Djava.class.path="
-    classpath_args = [arg for arg in jvm_args if arg.startswith(classpath_prefix)]
-    jvm_args = [arg for arg in jvm_args if arg not in classpath_args]
-
-    # Combine classpaths into a single list.
-    classpath = [
-        el
-        for arg in classpath_args
-        for el in arg[len(classpath_prefix):].split(os.path.pathsep)
-    ]
-
-    # Set JAVA_HOME to encourage use of the intended JVM.
-    # HACK: Assume the JVM library is nestled beneath a `lib` folder.
-    p = Path(libjvm_path).absolute().parent
-    while p.name != "lib" and p != p.parent:
-        p = p.parent
-    os.environ["JAVA_HOME"] = str(p.parent)
-
-    #scyjava.config.add_classpath(*scyjava.config.find_jars(app_dir))
-    scyjava.config.add_classpath(*classpath)
-    scyjava.start_jvm(jvm_args)
-
-    # Initialize ImageJ, wrapping the local Fiji directory.
-    # NB: It's OK to pass `interactive` always, because when the
-    # --headless flag is given, Fiji still ends up in headless mode.
-    ij = imagej.init(app_dir, mode="interactive")
-
-    # Let the Script Editor support Python via scyjava/PyImageJ.
-    scyjava.enable_python_scripting(ij.context())
-
-    # Show the user interface.
-    ij.ui().showUI()
-
-    return ij
-
-
-ij = launch_fiji()
-
-if not in_interactive_inspect_mode():
-    # We're not in interactive mode, so we need to block
-    # to prevent the entire process from shutting down.
-    from time import sleep
-    while True:
-        sleep(0.1)

fiji/fiji-linux64/Fiji.app/config/jaunch/fiji.toml

@@ -1,322 +0,0 @@
-# *** Welcome to the Fiji launcher's configuration file! ***
-#
-# The Fiji launcher is built on Jaunch (https://github.com/scijava/jaunch).
-#
-# The contents below define Fiji's particular launcher behavior and features,
-# on top of Jaunch's "sensible default" functionality.
-#
-# See the common.toml file for more details about Jaunch configuration.
-
-jaunch-version = 1
-
-program-name = 'Fiji'
-
-includes = ['jvm.toml', 'python.toml']
-
-supported-options = [
-    # General options
-    '--default-gc|do not use advanced garbage collector settings by default\n(-XX:+UseG1GC)',
-    '--gc-g1|use the G1 garbage collector',
-    '--debug-gc|show debug info about the garbage collector on stderr',
-    '--no-splash|suppress showing a splash screen upon startup',
-    '--jdb|launch the jdb debugger',
-
-    # Fiji-specific options
-    '--python|launch in Python mode',
-    '--no-python|do not launch in Python mode',
-    '--allow-multiple|do not reuse existing Fiji instance',
-    '--info|informational output',
-    '--plugins=<dir>|use <dir> to discover plugins',
-    '--run <plugin> [<arg>]|run <plugin> in Fiji, optionally with arguments',
-    '--edit [<file>...]|edit the given file in the script editor',
-
-    # Options to run programs other than Fiji
-    '--update|start the command-line version of the Updater',
-    '--main-class=<class name>|start the given class instead of Fiji',
-
-    # Windows things
-    '--console,--attach-console|attempt to attach output to the calling console',
-    '--new-console|ensure the launch of a new, dedicated console for output',
-    '--set-icon=<exe-file>,<ico-file>|add/replace the icon of the given program', #NO
-
-# Nico: NEED: execute a script with parameters
-# ./ImageJ-linux64 --headless --console --run hello.py 'name="Mr Kraken"'
-# Can we simplify this further?
-]
-
-modes = [
-  # Decide on launch mode: Python or Java?
-
-  # Interpolate cfg.launch-mode var to set a starting LAUNCH: hint.
-  'LAUNCH:${cfg.launch-mode}',
-  # If --python given, force PYTHON mode.
-  '--python|LAUNCH:PYTHON',
-  '--python|!LAUNCH:JVM',
-  # If --no-python given, force JVM mode.
-  '--no-python|LAUNCH:JVM',
-  '--no-python|!LAUNCH:PYTHON',
-
-  # Set INFO level logging for the command line Updater.
-  '--update|--info',
-
-  # Are we launching with an alternative main class?
-  # This list should match the one in jvm.main-class below.
-  '--jdb|MODE:custom-main',
-  '--update|MODE:custom-main',
-  '--main-class|MODE:custom-main',
-
-  # Disable the splash screen when running a different
-  # main class, or when --no-splash or --headless is given.
-  'MODE:custom-main|MODE:no-splash',
-  '--no-splash|MODE:no-splash',
-  '--headless|MODE:no-splash',
-]
-
-directives = [
-  'LAUNCH:JVM|!--dry-run|apply-update,INIT_THREADS',
-  'LAUNCH:PYTHON|!--dry-run|apply-update,INIT_THREADS',
-]
-
-# /============================================================================\
-# |                              CONFIG DEFAULTS                               |
-# \============================================================================/
-
-cfg.max-heap = '75%'
-cfg.launch-mode = 'JVM'
-
-# /============================================================================\
-# |                               PYTHON CONFIG                                |
-# \============================================================================/
-
-python.version-min = '3.9'
-
-python.packages = [
-  'pyimagej>=1.4.1',
-  'scyjava>=1.12.0',
-]
-
-python.script-path = ['${app-dir}/config/jaunch/fiji.py']
-
-python.main-args = [
-    '${jvm.libjvmPath}',
-    '@{jvm.runtimeArgs}',
-    '--',
-    '${jvm.mainClass}',
-    # Note: Jaunch appends @{python.mainArgs}, which will match.
-    #'@{jvm.mainArgs}',
-]
-
-# /============================================================================\
-# |                                JAVA CONFIG                                 |
-# \============================================================================/
-
-jvm.version-min = '8'
-
-jvm.classpath = [
-    # Construct the classpath.
-    '${app-dir}/jars/*.jar',
-    '${app-dir}/jars/*/*.jar',
-    '--plugins|${plugins}/*.jar'
-    '--plugins|${plugins}/*/*.jar'
-    '!--plugins|${app-dir}/plugins/*.jar',
-    '!--plugins|${app-dir}/plugins/*/*.jar',
-    #'${user.home}/.plugins/*.jar',
-    #'${user.home}/.plugins/*/*.jar',
-    #'${user.home}/.share/fiji/jars/*.jar',
-    #'/usr/local/share/fiji/jars/*.jar',
-    '--main-class|.', # Weird behavior, but it's what the ImageJ Launcher does.
-]
-
-jvm.max-heap = '${cfg.max-heap}'
-
-jvm.runtime-args = [
-    '--info|-Dscijava.log.level=info',
-    '--debug|-Dij.debug=true',
-    '--debug|-Dscijava.log.level=debug',
-
-    # In https://forum.image.sc/t/88620, acardona wrote:
-    # > When running in a machine with many CPU cores (like 64, or 256) and lots
-    # > of RAM (e.g., more than 100 GB, like 500 GB of heap size as defined by -Xmx),
-    # > I find that the concurrent garbage collector (G1 GC) works *a lot better*.
-    '!--default-gc|JAVA:6+|-XX:+UseG1GC',
-    # Handle --gc-g1 option.
-    '--gc-g1|-XX:+UseCompressedOops',
-    '--gc-g1|-XX:+UnlockExperimentalVMOptions',
-    '--gc-g1|-XX:+UseG1GC',
-    '--gc-g1|-XX:NewRatio=5',
-
-    # Handle --debug-gc option.
-    '--debug-gc|-verbose:gc',
-
-    # If running a custom main class, do not patch ImageJ.
-    'MODE:custom-main|-Dpatch.ij1=false',
-
-    # Enable SciJava logging in updater mode.
-    '--update|-Dscijava.log.level=info',
-
-    # For JavaFX - see https://github.com/apposed/jaunch/issues/51
-    #
-    # For now, we add only the platform-specific JAR subfolders,
-    # and explicitly enumerate the JavaFX modules.
-    #
-    # What would be nice to do is add everything to the module path:
-    #
-    #   --module-path jars --add-modules=ALL-MODULE-PATH
-    #
-    # Unfortunately, it is too brittle: it generates an automatic module name for each
-    # unmodularized JAR on the module path, even if the resultant name is invalid:
-    #
-    #   Error occurred during initialization of boot layer
-    #   java.lang.module.FindException: Unable to derive module descriptor for .../Fiji/jars/compiler-interface-1.3.5.jar
-    #   Caused by: java.lang.IllegalArgumentException: compiler.interface: Invalid module name: 'interface' is not a Java identifier
-    #
-    # In the longer term, we could avoid this issue by placing modularized
-    # JARs into a separate subtree -- perhaps `modules` instead of `jars`?
-    # The Updater would then need to grok the modules/<platform> subdirs, though.
-
-    'JAVA:9+|OS:LINUX|ARCH:ARM64|--module-path=${app-dir}/jars/linux-arm64',
-    'JAVA:9+|OS:LINUX|ARCH:X64|--module-path=${app-dir}/jars/linux64',
-    'JAVA:9+|OS:LINUX|ARCH:X86|--module-path=${app-dir}/jars/linux32',
-    'JAVA:9+|OS:MACOSX|ARCH:ARM64|--module-path=${app-dir}/jars/macos-arm64',
-    'JAVA:9+|OS:MACOSX|ARCH:X64|--module-path=${app-dir}/jars/macos64',
-    'JAVA:9+|OS:WINDOWS|ARCH:ARM64|--module-path=${app-dir}\jars\win-arm64',
-    'JAVA:9+|OS:WINDOWS|ARCH:X64|--module-path=${app-dir}\jars\win64',
-    'JAVA:9+|OS:WINDOWS|ARCH:X86|--module-path=${app-dir}\jars\win32',
-
-    # Give the SciJava app-launcher permission to unlock reflection on modularized code.
-    'JAVA:9+|--add-opens=java.base/java.lang=ALL-UNNAMED',
-
-    # TODO: Figure out why (some of?) these are still needed to squelch errors.
-    # sc.fiji.compat.DefaultFijiService uses XToolkit.awtAppClassName
-    'JAVA:9+|OS:LINUX|--add-opens=java.desktop/sun.awt.X11=ALL-UNNAMED',
-    # TODO: document where this happens on macOS.
-    'JAVA:9+|OS:MACOSX|--add-opens=java.desktop/com.apple.eawt=ALL-UNNAMED',
-     # net.imagej.patcher.LegacyInjector uses ClassLoader.findLoadedClass
-     # javassist.util.proxy.SecurityActions uses ClassLoader.defineClass
-     'JAVA:9+|--add-opens=java.base/java.lang=ALL-UNNAMED',
-     # For org.apache.arrow - TODO: document exactly why
-     'JAVA:9+|--add-opens=java.base/java.nio=ALL-UNNAMED',
-     # org.scijava.util.SizeableArrayList uses ArrayList.size
-     'JAVA:9+|--add-opens=java.base/java.util=ALL-UNNAMED',
-     # com.jogamp.nativewindow.awt.AppContextInfo uses sun.awt.AppContext
-     'JAVA:9+|--add-opens=java.desktop/sun.awt=ALL-UNNAMED',
-     #  ini.trakem2.Project.openFSProject uses javax.swing.JTree.expandedState
-     'JAVA:9+|--add-opens=java.desktop/javax.swing=ALL-UNNAMED',
-     # For accessing internal Swing UI classes used by BVV - TODO: document exactly where
-     'JAVA:9+|--add-opens=java.desktop/sun.swing=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.desktop/com.sun.java.swing=ALL-UNNAMED',
-     # HACK: For fiji.debugging.Object_Inspector
-     # The Object_Inspector could end up reflecting anything, so this doesn't
-     # make it work in all cases, but it helps for inspecting AWT/Swing windows.
-     'JAVA:9+|--add-opens=java.desktop/java.awt=ALL-UNNAMED',
-     # For scenery - TODO: document exactly why
-     #'JAVA:9+|--add-opens=java.base/java.lang=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/java.lang.invoke=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/java.lang.reflect=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/java.net=ALL-UNNAMED',
-     #'JAVA:9+|--add-opens=java.base/java.nio=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/java.time=ALL-UNNAMED',
-     #'JAVA:9+|--add-opens=java.base/java.util=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
-     'JAVA:9+|--add-opens=java.base/sun.util.calendar=ALL-UNNAMED',
-
-    # Avoid Jython's huge startup cost.
-    '-Dpython.cachedir.skip=true',
-
-    # Set ImageJ's plugins.dir property.
-    '--plugins|-Dplugins.dir=${plugins}',
-    '!--plugins|-Dplugins.dir=${app-dir}',
-
-    # Set application directory properties.
-    '-Dimagej.dir=${app-dir}',
-    '-Dij.dir=${app-dir}',
-    '-Dfiji.dir=${app-dir}',
-
-    # Set application executable properties.
-    '-Dfiji.executable=${executable}',
-    '-Dij.executable=${executable}',
-
-    # TODO: is fiji.defaultLibPath property necessary for any reason?
-
-    # Set up platform-specific native library paths.
-    # Regarding the setting of jna.library.path, see:
-    # https://github.com/scijava/scijava-common/pull/438
-    'OS:LINUX|ARCH:ARM64|-Djava.library.path=${app-dir}/lib/linux-arm64',
-    'OS:LINUX|ARCH:ARM64|-Djna.library.path=${app-dir}/lib/linux-arm64',
-    'OS:LINUX|ARCH:X64|-Djava.library.path=${app-dir}/lib/linux64',
-    'OS:LINUX|ARCH:X64|-Djna.library.path=${app-dir}/lib/linux64',
-    'OS:LINUX|ARCH:X86|-Djava.library.path=${app-dir}/lib/linux32',
-    'OS:LINUX|ARCH:X86|-Djna.library.path=${app-dir}/lib/linux32',
-    'OS:MACOSX|ARCH:ARM64|-Djava.library.path=${app-dir}/lib/macos-arm64',
-    'OS:MACOSX|ARCH:ARM64|-Djna.library.path=${app-dir}/lib/macos-arm64',
-    'OS:MACOSX|ARCH:X64|-Djava.library.path=${app-dir}/lib/macos64',
-    'OS:MACOSX|ARCH:X64|-Djna.library.path=${app-dir}/lib/macos64',
-    'OS:WINDOWS|ARCH:ARM64|-Djava.library.path=${app-dir}\lib\win-arm64',
-    'OS:WINDOWS|ARCH:ARM64|-Djna.library.path=${app-dir}\lib\win-arm64',
-    'OS:WINDOWS|ARCH:X64|-Djava.library.path=${app-dir}\lib\win64',
-    'OS:WINDOWS|ARCH:X64|-Djna.library.path=${app-dir}\lib\win64',
-    'OS:WINDOWS|ARCH:X86|-Djava.library.path=${app-dir}\lib\win32',
-    'OS:WINDOWS|ARCH:X86|-Djna.library.path=${app-dir}\lib\win32',
-
-    # Set properties favored by the the SciJava app-launcher.
-    # See https://github.com/scijava/app-launcher#readme
-    '-Dscijava.app.name=Fiji',
-    '-Dscijava.app.directory=${app-dir}',
-    '!MODE:no-splash|!OS:WINDOWS|-Dscijava.app.splash-image=${app-dir}/images/icon.png',
-    '!MODE:no-splash|OS:WINDOWS|-Dscijava.app.splash-image=${app-dir}\images\icon.png',
-    '-Dscijava.app.java-version-minimum=1.8',
-    '-Dscijava.app.java-version-recommended=1.8.0_172',
-    '-Dscijava.app.look-and-feel=com.formdev.flatlaf.FlatLightLaf',
-    'OS:WINDOWS|-Dscijava.app.config-file=${app-dir}\config\jaunch\fiji.cfg',
-    '!OS:WINDOWS|-Dscijava.app.config-file=${app-dir}/config/jaunch/fiji.cfg',
-    'OS:LINUX|ARCH:ARM64|-Dscijava.app.java-root=${app-dir}/java/linux-arm64',
-    'OS:LINUX|ARCH:X64|-Dscijava.app.java-root=${app-dir}/java/linux64',
-    'OS:LINUX|ARCH:X86|-Dscijava.app.java-root=${app-dir}/java/linux32',
-    'OS:MACOSX|ARCH:ARM64|-Dscijava.app.java-root=${app-dir}/java/macos-arm64',
-    'OS:MACOSX|ARCH:X64|-Dscijava.app.java-root=${app-dir}/java/macos64',
-    'OS:WINDOWS|ARCH:ARM64|-Dscijava.app.java-root=${app-dir}\java\win-arm64',
-    'OS:WINDOWS|ARCH:X64|-Dscijava.app.java-root=${app-dir}\java\win64',
-    'OS:WINDOWS|ARCH:X86|-Dscijava.app.java-root=${app-dir}\java\win32',
-    '-Dscijava.app.java-links=https://downloads.imagej.net/java/jdk-urls.txt',
-    'OS:LINUX|ARCH:ARM64|-Dscijava.app.java-platform=linux-arm64',
-    'OS:LINUX|ARCH:X64|-Dscijava.app.java-platform=linux64',
-    'OS:LINUX|ARCH:X86|-Dscijava.app.java-platform=linux32',
-    'OS:MACOSX|ARCH:ARM64|-Dscijava.app.java-platform=macos-arm64',
-    'OS:MACOSX|ARCH:X64|-Dscijava.app.java-platform=macos64',
-    'OS:WINDOWS|ARCH:ARM64|-Dscijava.app.java-platform=win-arm64',
-    'OS:WINDOWS|ARCH:X64|-Dscijava.app.java-platform=win64',
-    'OS:WINDOWS|ARCH:X86|-Dscijava.app.java-platform=win32',
-
-    # Make SciJava startup less brittle.
-    '-Dscijava.context.strict=false',
-
-    # Enable JavaFX's JavaScript engine.
-    '-Djavafx.allowjs=true',
-
-    # Enable AWT/Swing's HiDPI scaling.
-    '-Dsun.java2d.uiScale=true',
-
-    # Avoid the following error message on Windows:
-    #
-    #   console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
-    #
-    # See https://github.com/imagej/imagej-launcher/issues/56
-    '-Dpython.console.encoding=UTF-8',
-]
-
-jvm.main-class = [
-    # This list should match the one in modes above.
-    '--jdb|com.sun.tools.example.debug.tty.TTY',
-    '--update|net.imagej.updater.CommandLine',
-    '--main-class|${main-class}',
-    'org.scijava.launcher.ClassLauncher',
-]
-
-jvm.main-args = [
-    # Pass the actual main class to the ClassLauncher as an argument.
-    '!MODE:custom-main|net.imagej.Main',
-
-    # The -batch flag is required when --headless is given.
-    '--headless|!MODE:custom-main|-batch',
-]

fiji/fiji-linux64/Fiji.app/config/jaunch/fiji.txt

@@ -1,32 +0,0 @@
-The ImageJ Launcher (a.k.a. the Fiji Launcher) program has been replaced with a
-new launcher named Jaunch.
-
-I made a concerted effort to preserve backward compatibility as much as
-possible. As such, most features of the previous launcher still work in the
-same manner.
-
-However, the following features of the ImageJ Launcher are no longer supported:
-
-* Launching in "Fiji1" mode (fiji.Main).
-
-* Launching in "IJ1" mode without ImageJ2 support.
-  A separate `imagej` launcher configuration now exists for this use case.
-  But it does not use the ImageJ.cfg file; you must edit imagej.toml.
-
-* Launching versions of ImageJ2 before 2.0.0-beta-8
-  (released 2014-05-16) when the component+package structure was finalized.
-
-* The undocumented `--tools-jar` nor `--only-tools-jar` options.
-
-* Usage of Info.plist `<key>` elements to get and set launch configuration
-  parameters on macOS. We need to keep the entire Fiji.app immutable in the
-  future, to facilitate code signing for better distribution mechanisms.
-
-* Best-effort automatic detection of headless mode on macOS and Linux.
-
-* "Falling back to system Java" i.e. launching Java in a subprocess.
-  Jaunch always uses libjvm functions.
-
-* TODO: Decide about all the various `net.imagej.launcher.*` features...
-
-See also https://github.com/scijava/jaunch/issues.

fiji/fiji-linux64/Fiji.app/config/jaunch/jaunch-linux-x64

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b3f9136999f2d1c2d4ee845dad29acb707392e1173eea988da3fe56ad69f98bb
-size 1694408

fiji/fiji-linux64/Fiji.app/config/jaunch/jvm.toml

@@ -1,649 +0,0 @@
-# Shared Jaunch configuration for JVM-based programs.
-#
-# See the common.toml file for an introduction to Jaunch configuration.
-
-includes = ['common.toml']
-
-# ==============================================================================
-# JVM-specific Jaunch options.
-#
-# Two quick examples from the below list:
-#
-# 1. The --headless option configures Jaunch to pass the flag -Djava.awt.headless=true
-#    to the JVM. This makes it friendlier for CLI users to launch your application in
-#    headless mode, without knowing anything about the Java platform specifically.
-#
-# 2. Similarly, --heap=1234m (aliased also to --mem and --memory) will be transformed
-#    into a -Xmx1234m argument to the JVM, so that users have an easier-to-remember
-#    option for setting the max heap size, without memorizing Java's -Xmx terminology.
-#
-# (In both of these examples, the transformations described are defined within the
-# jvm.runtime-args section toward the bottom of the file. Be patient, we'll get there!)
-
-supported-options = [
-    '--java-home=<path>|specify Java installation path explicitly',
-    '--print-class-path,--print-classpath|print runtime classpath elements',
-    '--print-java-home|print path to the selected Java',
-    '--print-java-info|print information about the selected Java',
-    "--heap,--mem,--memory=<amount>|set Java's heap size to <amount> (e.g. 512M or 64%)",
-    '--class-path,--classpath,-classpath,--cp,-cp=<path>|append <path> to the class path',
-    "--ext=<path>|set Java's extension directory to <path>",
-    '--debugger=<port>[,suspend]|start Java in a mode so an IDE/debugger can attach to it',
-]
-
-# ==============================================================================
-# JVM-specific modes:
-#
-# * LAUNCH:JVM - when set, JVM will be included in the directives.
-
-#modes = ['LAUNCH:JVM']
-
-# ==============================================================================
-# JVM-specific directives:
-#
-# * JVM                - Launches the main program using the Java Virtual Machine.
-# * print-class-path   - Print out the runtime classpath, one element per line.
-# * print-java-home    - Print out the path to the chosen Java installation.
-# * print-java-info    - Print out all the details of the chosen Java installation,
-#                        including not only its path, but also the distro, version,
-#                        operating system, CPU architecture, and other metadata fields.
-
-directives = [
-    'LAUNCH:JVM|JVM',
-    '--print-class-path|print-class-path,ABORT',
-    '--print-java-home|print-java-home,ABORT',
-    '--print-java-info|print-java-info,ABORT',
-]
-
-# ==============================================================================
-# jvm.enabled
-# ==============================================================================
-# Set this to true to enable searching for and launching with a JVM.
-
-jvm.enabled = true
-
-# ==============================================================================
-# jvm.recognized-args
-# ==============================================================================
-# The list of arguments that Jaunch will recognize as belonging to the JVM,
-# rather than to the `String[] args` of your application's main method.
-#
-# These are used to guess, when the minus-minus divider (--) is absent,
-# whether each arg is a JVM (runtime) one or a main one.
-#
-# The asterisk wildcard symbol (*) is allowed as a suffix,
-# if you want to match all arguments with a particular prefix.
-#
-# About main arguments: Jaunch's philosophy is to remain agnostic of the options
-# your application supports, rather than trying to constrain them in its configuration
-# and checking them itself. As such, it is your application's responsibility to emit
-# error messages as appropriate if it encounters displeasing arguments.
-#
-# For example, suppose the user invokes:
-#
-#     ./fizzbuzz 1 2 3 4 5 -Xms1g
-#
-# Because '-X*' is on the jvm.recognized-args list out of the box,
-# Jaunch will translate this invocation to:
-#
-#     java -Xms1g org.fizzbuzz.FizzBuzz 1 2 3 4 5
-#
-# Even though the Java argument appears after the main arguments. Users can mix
-# and match to their hearts' content, being as sloppy as they want, and Jaunch will
-# sort out the mess. As long as the JVM args are on the list here, of course.
-
-jvm.recognized-args = [
-    '-?',                        # 8, 11, 17, 21
-    '-D*',                       # 8, 11, 17, 21
-    '-X',                        # 8, 11, 17, 21
-    '-X*',                       # 8, 11, 17, 21
-    '-agentlib:*',               # 8, 11, 17, 21
-    '-agentpath:*',              # 8, 11, 17, 21
-    '-classpath <>',             # 8, 11, 17, 21
-    '-cp <>',                    # 8, 11, 17, 21
-    '-d <>',                     #    11, 17, 21
-    '-d32',                      # 8
-    '-d64',                      # 8
-    '-da',                       # 8, 11, 17, 21
-    '-da:*',                     # 8, 11, 17, 21
-    '-disable-@files',           #    11, 17
-    '-disableassertions',        # 8, 11, 17, 21
-    '-disableassertions:*',      # 8, 11, 17, 21
-    '-disablesystemassertions',  # 8, 11, 17, 21
-    '-dsa',                      # 8, 11, 17, 21
-    '-ea',                       # 8, 11, 17, 21
-    '-ea:*',                     # 8, 11, 17, 21
-    '-enableassertions',         # 8, 11, 17, 21
-    '-enableassertions:*',       # 8, 11, 17, 21
-    '-enablesystemassertions',   # 8, 11, 17, 21
-    '-esa'                       # 8, 11, 17, 21
-    '-h',                        #    11, 17, 21
-    '-help',                     # 8, 11, 17, 21
-    '-jar <>',                   # 8, 11, 17, 21
-    '-javaagent:*',              # 8, 11, 17, 21
-    '-jre-restrict-search',      # 8
-    '-m <>',                     #    11, 17, 21
-    '-no-jre-restrict-search',   # 8
-    '-p <>',                     #    11, 17, 21
-    '-server',                   # 8
-    '-showversion',              # 8, 11, 17, 21
-    '-splash:*',                 # 8, 11, 17, 21
-    '-truffle',                  #        17
-    '-verbose:class',            # 8, 11, 17, 21
-    '-verbose:gc',               # 8, 11, 17, 21
-    '-verbose:jni',              # 8, 11, 17, 21
-    '-verbose:module',           #    11, 17, 21
-    '-version',                  # 8, 11, 17, 21
-    '-version:*',                # 8
-    '--add-exports <>',          #    11, 17, 21
-    '--add-exports=*',           #    11, 17, 21
-    '--add-modules <>',          #    11, 17, 21
-    '--add-modules=*',           #    11, 17, 21
-    '--add-opens <>',            #    11, 17, 21
-    '--add-opens=*',             #    11, 17, 21
-    '--add-reads <>',            #    11, 17, 21
-    '--add-reads=*',             #    11, 17, 21
-    '--class-path <>',           #    11, 17, 21
-    '--class-path=*',            #    11, 17, 21
-    '--describe-module <>',      #    11, 17, 21
-    '--describe-module=*',       #    11, 17, 21
-    '--disable-@files',          #            21
-    '--dry-run',                 #    11, 17, 21
-    '--enable-native-access <>', #        17, 21
-    '--enable-native-access=*',  #        17, 21
-    '--enable-preview',          #    11, 17, 21
-    '--help',                    #    11, 17, 21
-    '--help-extra',              #    11, 17, 21
-    '--illegal-access <>',       #    11
-    '--illegal-access=*',        #    11
-    '--limit-modules <>',        #    11, 17, 21
-    '--limit-modules=*',         #    11, 17, 21
-    '--list-modules',            #    11, 17, 21
-    '--module <>',               #    11, 17, 21
-    '--module=*',                #    11, 17, 21
-    '--module-path <>',          #    11, 17, 21
-    '--module-path=*',           #    11, 17, 21
-    '--patch-module <>',         #    11, 17, 21
-    '--patch-module=*',          #    11, 17, 21
-    '--show-module-resolution',  #    11, 17, 21
-    '--show-version',            #    11, 17, 21
-    '--source <>',               #    11, 17, 21
-    '--source=*',                #    11, 17, 21
-    '--upgrade-module-path <>',  #    11, 17, 21
-    '--upgrade-module-path=*',   #    11, 17, 21
-    '--validate-modules',        #    11, 17, 21
-    '--version',                 #    11, 17, 21
-    '@*',                        #    11, 17, 21
-]
-
-# ==============================================================================
-# jvm.allow-weird-runtimes
-# ==============================================================================
-# Whether to attempt to launch with mysterious flavors of the JVM.
-#
-# When Jaunch discovers a Java installation on the user's system, it tries very hard
-# to understand the details of that installation, including Java version, distribution
-# (see `jvm.distros-allowed` and `jvm.distros-blocked` below), operating system, and
-# CPU architecture, so that it can respect the constraints defined in this config file.
-#
-# However, the variability across JVM distributions is actually quite a lot:
-#
-# * The vast majority of distros include a file named 'release' with important metadata
-#   fields inside. But a few distros are missing that file (e.g. Corretto 1.8.0_265-b01
-#   for x64 Linux), and a few others are missing needed metadata fields (e.g. Liberica
-#   1.8.0_392 for x64 Linux, which is missing IMPLEMENTOR), or they might put something
-#   stupid as a value (e.g. JBRSDK 11.0.6 for x64 Linux, which has IMPLEMENTOR="N/A").
-#
-# * For that reason, Jaunch also parses the directory name of the installation, trying
-#   to extract this information. But the naming schemes across distro are also very
-#   diverse and sometimes uninformative: e.g. JBRSDK 11.0.6 for x64 Linux, which has the
-#   vague folder name of "jbrsdk" with no version, or JBRSDK 11.0.8 for x64 Linux, which
-#   has the nested folder name "jbrsdk_11.0.8_x64/jbr" making the final directory name
-#   "jbr" still with no version, or JBRSDK 8 for Linux, which has no directory prefix at
-#   all. And of course users and packaging scripts can rename the JVM root directory to
-#   anything, corrupting this information in the process.
-#
-# * As a final measure, when needed, Jaunch invokes the Java installation's bin/java on
-#   a small Java program that prints out all key=value pairs of System.getProperties(),
-#   paying particular attention to java.version, java.vendor, and java.vendor.version.
-#   This is the slowest but most reliable way to gather metadata about an installation.
-#   But it's not a guaranteed solution either: for example, JVMs bundled up by jpackage
-#   are placed in a lib/runtime directory without a bin folder! So no bin/java.
-#
-# As such, it is possible for all of Jaunch's efforts to be in vain, and to end up
-# trying to decide whether to launch with some mystery-flavored JVM. In such scenarios,
-# the jvm.allow-weird-runtimes flag comes to the rescue, telling Jaunch whether to allow
-# it (true), or give up and complain (false). Hopefully, your users will never know the
-# difference, as long as they have well-behaved distros, and/or you ship a good distro
-# with your application. But just in case, give a think to how you want this to behave.
-
-jvm.allow-weird-runtimes = true
-
-# ==============================================================================
-# jvm.version-min, jvm.version-max
-# ==============================================================================
-# Acceptable range of Java versions to match.
-#
-# These two fields let you constrain the minimum and maximum Java versions respectively
-# that your application supports. This information will be used when searching the
-# system for appropriate JVM installations. If a JVM is successfully discovered, but
-# then found to be outside these constraints, it is discarded and the search continues.
-# For installations whose version cannot be determined, what Jaunch does will depend on
-# the jvm.allow-weird-runtimes boolean setting above.
-#
-# The most common use of these fields is to specify major versions alone (e.g.
-# `jvm.version-min = '11'`), but Jaunch does make a best effort to compare version
-# strings digit by digit, so you could try `jvm.version-min = '1.8.0.101'` if you
-# like to live dangerously. YMMV, though.
-#
-# "But what syntax exactly should I use to specify these versions?" you might wonder.
-# Excellent question! To answer that, let's have some background:
-#
-# As Ralph Waldo Emerson wrote, a foolish consistency is the hobgoblin of little minds.
-# Never has that belief been put into action more fervently than it has with the Java
-# versioning scheme, which has a fraught and confusing history:
-#
-# * The first stable release of Java, 1.0.2, was also called Java 1.
-#
-# * The 1.2 release was marketed as the Java 2 Platform, Standard Edition (J2SE).
-#
-# * The 1.5 release was marketed as Java SE 5, with a "developer version" of 1.5
-#   and a "product version" of 5.0.
-#
-# * This dual versioning scheme continued through versions 1.6, 1.7, and 1.8,
-#   which were also known as 6, 7 and 8 respectively -- although the '1.' prefix
-#   (at least in my anecdotal experience) decreased in prominence over time.
-#
-# * There is also a baffling convention that Java 8 specifically uses where
-#   version 1.8.0_XYZ -- which is also written as 8.0_XYZ or 8.0.XYZ -- is
-#   frequently expressed as 8uXYZ.
-#
-# * With the release of Java 9, the '1.' prefix was finally officially dropped.
-#
-# * Nonetheless, for backwards compatibility with old assumptions, you might still
-#   see a '1.' here or there, such as the /usr/lib/jvm folder on Debian/Ubuntu.
-#
-# You can read more details at https://en.wikipedia.org/wiki/Java_version_history.
-#
-# Check out this exciting table of Google search results (excluding Minecraft):
-#
-#   x | "Java 1.x" |   "Java x" | Ratio | Comments
-# :--:|-----------:|-----------:|-------|---------
-#   0 |     78,400 |    229,000 |     2 |
-#   1 |    119,000 |  3,510,000 |    29 |
-#   2 |     71,000 |  2,870,000 |    40 | "Java 2 SE" term skews results?
-#   3 |     62,800 |  1,130,000 |    17 |
-#   4 |    155,000 |    752,000 |     4 |
-#   5 |    328,000 |  1,080,000 |     3 |
-#   6 |    264,000 |  1,330,000 |     5 |
-#   7 |    223,000 |  1,810,000 |     8 |
-#   8 |    798,000 | 24,200,000 |    30 | LTS release
-#   9 |     11,200 |  1,250,000 |   111 | 1.x scheme discontinued
-#  10 |      4,790 |    604,000 |   126 |
-#  11 |      9,390 |  1,860,000 |   198 | LTS release
-#  12 |         10 |    360,000 | 36000 | 10? Really?
-#  13 |      2,140 |    315,000 |   147 |
-#  14 |      2,330 |    356,000 |   152 |
-#  15 |      2,010 |    294,000 |   146 |
-#  16 |      3,630 |    382,000 |   105 |
-#  17 |      3,000 |  1,110,000 |   370 | LTS release
-#  18 |      1,790 |    282,000 |   157 |
-#  19 |      9,360 |    332,000 |    35 |
-#  20 |     14,700 |    329,000 |    22 |
-#  21 |        820 |  1,050,000 |  1280 | LTS release
-#
-# Who knows what (if anything) this table proves, but it's probably Numberwang!
-#
-# So back to the key question: what numbers should you write for the min and max?
-# Use the so-called "developer version" in all cases, with dots only as separators:
-#
-# * For Java 8 and earlier, prepend the '1.' portion.
-# * For Java 9 and later, don't.
-#
-# So if you want 1.8.0_101 (a.k.a. 8u101), write '1.8.0.101', not '8.0.101'.
-# If you want 11.0.8, write '11.0.8', not '1.11.0.8'.
-#
-# As a kindness, when Jaunch sees a major version digit less than 9, it prepends the
-# '1.' prefix on your behalf. So you can write e.g. `jvm.version-min = '8'` if you
-# really want to. Jaunch also strips the '1.' leading digit when the subsequent minor
-# version digit is 9 or more. So write '1.11.0.8' if you must! But know that in doing
-# so, you stand opposed to the hallowed official versioning scheme, a heretic in the
-# eyes of Java developers everywhere. You have been warned!
-
-#jvm.version-min = '8' # hobgoblin!
-#jvm.version-max = '21'
-
-# ==============================================================================
-# jvm.distros-allowed, jvm.distros-blocked
-# ==============================================================================
-# Acceptable and unacceptable distributions/vendors/flavors of Java to match.
-#
-# These two fields let you constrain which Java distributions are OK to use and which
-# are not, respectively. For distros matching neither the allowlist nor blocklist,
-# what Jaunch does will depend on the jvm.allow-weird-runtimes boolean setting above.
-#
-# As of this writing, the following Java distributions have been tested:
-#
-# Distribution       | IMPLEMENTOR              | IMPLEMENTOR_VERSION prefix             | root folder slug
-# -------------------| -------------------------|----------------------------------------|-----------------
-# AdoptOpenJDK       | AdoptOpenJDK             | AdoptOpenJDK                           | adopt
-# Alibaba Dragonwell | Alibaba                  | (Alibaba Dragonwell Extended Edition)* | dragonwell
-# Amazon Corretto    | Amazon.com Inc.*         | Corretto*                              | corretto or amazon-corretto*
-# Azul Zulu          | Azul Systems, Inc.*      | Zulu*                                  | zulu
-# BellSoft Liberica  | BellSoft                 | <none>                                 | <none>
-# Eclipse Temurin    | Eclipse Adoptium         | Temurin                                | <none>
-# IBM Semuru         | IBM Corporation          | <none>                                 | <none>
-# JetBrains JBRSDK   | N/A or JetBrains s.r.o.* | JBRSDK*                                | jbrsdk*
-# Microsoft OpenJDK  | Microsoft                | Microsoft                              | <none>
-# OpenLogic OpenJDK  | OpenLogic                | OpenLogic-OpenJDK                      | openlogic-openjdk
-# GraalVM Community  | GraalVM Community        | <none>                                 | graalvm-ce or graalvm-community-openjdk
-# GraalVM Enterprise | Oracle Corporation       | <none>                                 | graalvm-jdk
-# Oracle Java SE     | Oracle Corporation       | <none>                                 | oracle*
-# Oracle OpenJDK     | Oracle Corporation       | <none>                                 | oracle*
-# SAP SapMachine     | SAP SE                   | SapMachine                             | sapmachine-jdk
-# Tencent KonaJDK    | Tencent*                 | TencentKonaJDK*                        | TencentKona
-# Ubuntu OpenJDK     | Ubuntu or Private Build  | <none>                                 | <none>
-#
-# An asterisk (*) means that that metadata field, and/or the release file itself, is
-# missing (or for the root folder, that there is no telltale slug) for some versions.
-# Generally speaking, metadata and naming have improved as Java has evolved; often it
-# is Java 8 versions of these distributions that have the most metadata/naming issues.
-#
-# As the table above shows, every observed distro has some telltale signs, with the
-# release file being more likely to provide useful information, but there are many
-# exceptions, so Jaunch uses all available sources when scrutinizing installations.
-#
-# For each line below, the initial part before the colon names the distro, and comma-
-# separated elements afterward define tokens used to detect that distro from extracted
-# metadata fields. Fields are downcased, then checked for substrings matching a token.
-#
-# Examples:
-#
-# * A root directory named 'jdk_corretto_8.x64' with no release file will be identified
-#   as Amazon Corretto, because the token 'corretto' appears in the root folder name.
-#
-# * A root directory named 'best-openjdk-ever' with a release file containing lines:
-#
-#       IMPLEMENTOR="Azul Systems, Inc."
-#       IMPLEMENTOR_VERSION="Zulu21.30+19-CRaC-CA"
-#
-#   will be identified as Azul Zulu, because the token 'azul' matches the IMPLEMENTOR.
-#
-# * A root directory named 'i-forgot-where-this-came-from' with a minimal release file
-#   missing the IMPLEMENTOR and IMPLEMENTOR_VERSION entries, and a jre/lib/rt.jar
-#   whose META-INF/MANIFEST.MF contains the lines:
-#
-#       Manifest-Version: 1.0
-#       Implementation-Title: Java Runtime Environment
-#       Implementation-Version: 1.8.0_392
-#       Specification-Vendor: Oracle Corporation
-#       Specification-Title: Java Platform API Specification
-#       Specification-Version: 1.8
-#       Created-By: 1.8.0_252 (Tencent)
-#       Implementation-Vendor: Tencent
-#
-#   will be identified as TencentKona, because Jaunch will invoke bin/java and
-#   see that the token 'tencent' matches the `java.vendor` system property.
-
-jvm.distros-allowed = [
-    'Alibaba Dragonwell:alibaba,dragonwell',
-    'Amazon Corretto:amazon,corretto',
-    'Azul Zulu:azul,zulu',
-    'Bellsoft Liberica:bellsoft,liberica',
-    'Eclipse Temurin:eclipse,adoptium,temurin',
-    'AdoptOpenJDK:adopt', # NB: Must follow Temurin, since adopt is a substring of adoptium.
-    'IBM Semuru:ibm,semuru',
-    'JetBrains JBRSDK:jetbrains,jbrsdk',
-    'Microsoft OpenJDK:microsoft',
-    'OpenLogic OpenJDK:openlogic',
-    'GraalVM Community:graalvm-c',
-    'GraalVM Enterprise:graalvm-jdk',
-    'Oracle Java SE / OpenJDK:oracle', # NB: Must follow GraalVM Enterprise, since 'oracle' appears there as well.
-    'SAP SapMachine:sapmachine',
-    'TencentKona:tencent,kona',
-    'Ubuntu OpenJDK:ubuntu',
-]
-
-jvm.distros-blocked = []
-
-# ==============================================================================
-# Developer aside: Right now, Jaunch only filters Java installations by distro,
-# version, OS, and CPU arch. But there are further criteria it could support:
-#
-# * Java Development Kit (JDK) vs. Java Runtime Environment (JRE).
-# * Availability of optional features such as CRaC or JavaFX/OpenJFX.
-# * Minimum and/or maximum versions of operating systems (Windows 11+).
-# * More complex version filtering rules, e.g. multiple version exclusion ranges.
-#
-# Implementing such additional criteria will be done according to user demand.
-# If you need these, open an issue: https://github.com/scijava/jaunch/issues/new
-
-# ==============================================================================
-# jvm.root-paths
-# ==============================================================================
-# Paths to check for Java installations.
-#
-# This is a list of directories where Jaunch might hope to find a Java installation.
-# Directories are checked sequentially until one is found that matches all criteria.
-#
-# This is also the first field where we see Jaunch's hints/rules system in action.
-# See the `modes` section of common.toml for an introduction to hints.
-#
-# The JVM runtime adds hints based on the Java installation selected:
-#
-# - JAVA:8 if the selected Java installation is version 8.
-# - JAVA:8+ if the selected Java installation is version 8 or later.
-# - JAVA:9 if the selected Java installation is version 9.
-# - JAVA:9+ if the selected Java installation is version 9 or later.
-# - and so on.
-#
-# Of course, Java hints will only be set after a Java installation matches,
-# so they won't work here in jvm.root-paths, nor in jvm.lib-suffixes.
-# But they can be useful in the jvm.runtime-args section to ensure Jaunch
-# passes JVM args only to those versions of the JVM that support them, such
-# as the JPMS-related flags like --add-opens which were introduced in Java 9.
-#
-# This is also the first field where we see Jaunch's variables in use:
-#
-#     '--java-home|${java-home}'
-#
-# Thanks to the above line, when the user passes '--java-home=/the-best-jdk', the
-# --java-home hint will be set, and the java-home variable will be set to /the-best-jdk.
-# So not only will the line match, but the root path to check will become /the-best-jdk.
-#
-# Similarly, variable expressions are also sourced from environment variables, so the
-# lines containing '${CONDA_PREFIX}' will use the CONDA_PREFIX environment variable.
-
-jvm.root-paths = [
-    '--java-home|${java-home}',                                                    # user override (CLI flag)
-    '!--system|${cfg.jvm-dir}',                                                    # read from <app>.cfg
-    '!--system|${app-dir}/lib/runtime',                                            # jpackage
-    '!--system|OS:LINUX|ARCH:ARM64|${app-dir}/java/linux-arm64/*',                 # bundled (Linux arm64)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/java/linux-x64/*',                     # bundled (Linux x86-64)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/java/linux-amd64/*',                   # bundled (Linux x86-64)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/java/linux64/*',                       # bundled (Linux x86-64)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/java/linux-x32/*',                     # bundled (Linux x86-32)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/java/linux-x86/*',                     # bundled (Linux x86-32)
-    '!--system|OS:LINUX|ARCH:X86|${app-dir}/java/linux32/*',                       # bundled (Linux x86-32)
-    '!--system|OS:LINUX|ARCH:X86|${app-dir}/java/linux/*',                         # bundled (Linux x86-32)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/java/macos-arm64/*/Contents/Home',  # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/java/macos-arm64/*',                # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/java/macosx-arm64/*/Contents/Home', # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/java/macosx-arm64/*',               # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macos64/*/Contents/Home',        # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macos64/*',                      # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macos/*/Contents/Home',          # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macos/*',                        # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macosx/*/Contents/Home',         # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macosx/*',                       # bundled (macOS x86-64)
-    # Fiji used to ship versions of OpenJDK 8 with a mangled directory structure.
-    # The mangling was done to work around limitations of the old ImageJ Launcher.
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/java/macosx/*/jre/Contents/Home',
-    '!--system|OS:WINDOWS|ARCH:ARM64|${app-dir}\java\windows-arm64\*',             # bundled (Windows arm64)
-    '!--system|OS:WINDOWS|ARCH:ARM64|${app-dir}\java\win-arm64\*',                 # bundled (Windows arm64)
-    '!--system|OS:WINDOWS|ARCH:X64|${app-dir}\java\windows-x64\*',                 # bundled (Windows x86-64)
-    '!--system|OS:WINDOWS|ARCH:X64|${app-dir}\java\win64\*',                       # bundled (Windows x86-64)
-    '!--system|OS:WINDOWS|ARCH:X86|${app-dir}\java\windows-x32\*',                 # bundled (Windows x86-32)
-    '!--system|OS:WINDOWS|ARCH:X86|${app-dir}\java\windows-x86\*',                 # bundled (Windows x86-32)
-    '!--system|OS:WINDOWS|ARCH:X86|${app-dir}\java\win32\*',                       # bundled (Windows x86-32)
-    '${JAVA_HOME}',                                                                # JAVA_HOME environment variable
-    '${CONDA_PREFIX}/pkgs/*jdk*/lib/jvm',                                          # Conda (openjdk 9+)
-    '${CONDA_PREFIX}/pkgs/*jdk*',                                                  # Conda (openjdk 8)
-    'OS:LINUX|/usr/lib/jvm/*',                                                     # Linux distro package manager (e.g. apt)
-    'OS:LINUX|/var/lib/flatpak/runtime/*jdk*/*/*/*/files/jvm/*',                   # Flatpak
-    'OS:LINUX|/snap/*jdk/*/jdk',                                                   # snap
-    'OS:LINUX|~/.sdkman/candidates/java/*',                                        # sdkman.io
-    '${CJDK_CACHE_DIR}/v*/jdks/*/*',                                               # github.com/cachedjdk/cjdk
-    '${XDG_CACHE_HOME}/cjdk/v*/jdks/*/*',                                          # github.com/cachedjdk/cjdk
-    'OS:LINUX|~/.cache/cjdk/v*/jdks/*/*',                                          # github.com/cachedjdk/cjdk
-    'OS:MACOSX|~/Library/Caches/cjdk/v*/jdks/*/*',                                 # github.com/cachedjdk/cjdk
-    'OS:WINDOWS|${LOCALAPPDATA}\cjdk\cache\v*\jdks\*\*',                           # github.com/cachedjdk/cjdk
-    'OS:WINDOWS|${USERPROFILE}\AppData\Local\cjdk\cache\v*\jdks\*\*',              # github.com/cachedjdk/cjdk
-    'OS:LINUX|~/.jdk/*',                                                           # github.com/jyksnw/install-jdk
-    'OS:LINUX|~/.jre/*',                                                           # github.com/jyksnw/install-jdk
-    'OS:MACOSX|/Library/Java/JavaVirtualMachines/*/Contents/Home',                 # Java 8+
-    'OS:MACOSX|/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home',  # JRE 8 by Oracle
-    'OS:MACOSX|${HOMEBREW_PREFIX}/Cellar/*jdk*/*/libexec/*.jdk/Contents/Home',     # Homebrew
-    'OS:MACOSX|/opt/homebrew/Cellar/*jdk*/*/libexec/*.jdk/Contents/Home',          # Homebrew (arm64 default)
-    'OS:MACOSX|/usr/local/Cellar/*jdk*/*/libexec/*.jdk/Contents/Home',             # Homebrew (x86-64 default)
-    'OS:WINDOWS|${ProgramFiles}\Java\*',                                           # System-wide install on Windows
-    'OS:WINDOWS|${ProgramFiles(x86)}\Java\*',                                      # System-wide install on Windows
-    'OS:WINDOWS|~\scoop\apps\*jdk*\*',                                             # Scoop openjdk, temurin-jdk, ...
-    'OS:WINDOWS|~\scoop\apps\mambaforge\*\envs\*\Library\lib\jvm',                 # Scoop mambaforge
-]
-
-# ==============================================================================
-# Developer aside: Right now, Jaunch does not utilize any programmatic ways
-# to discover Java root directories. But it could! In particular:
-#
-# - Windows: look for registry keys
-# - macOS: /usr/libexec/java_home -V
-# - Linux: /usr/sbin/update-java-alternatives -l
-#
-# We could invent schema elements for toggling use of these detection approaches.
-# But for now: YAGNI! File an issue or a pull request if you do need it.
-
-# ==============================================================================
-# jvm.lib-suffixes
-# ==============================================================================
-# List of places within a Java installation to look for the JVM library.
-#
-# For example, if the root directory currently being considered is
-# /the-best-jvm, and the current libjvm suffix line is lib/server/libjvm.so,
-# then Jaunch will check the path /the-best-jvm/lib/server/libjvm.so for the
-# library. If found, we have a winning Java installation!
-#
-# For macOS, the reason to prefer libjli.dylib over libjvm.dylib is that if
-# one dynamically loads libjvm.dylib via dlopen(), macOS helpfully pops up a
-# dialog box instructing the user to install Apple Java 6. At least: it did
-# so for many years, including for several OS versions where Apple Java 6 no
-# longer functioned properly. While it is possible that Apple has since changed
-# this problematic behavior, we keep using libjli.dylib because it still works,
-# and definitely avoids the problem on systems where that behavior is present.
-# Related reading: https://bugs.openjdk.org/browse/JDK-8064542
-#
-# Finally, perusing the list below, you may notice several entries beginning
-# with jre/. This nested folder is only present up to Java 8, nothing after.
-
-jvm.lib-suffixes = [
-    'OS:LINUX|lib/server/libjvm.so',                    # Java 9+
-    'OS:LINUX|ARCH:X64|lib/amd64/server/libjvm.so',     # Java 8 (64-bit)
-    'OS:LINUX|ARCH:X64|jre/lib/amd64/server/libjvm.so', # Java 8 (64-bit)
-    'OS:LINUX|ARCH:X86|lib/i386/server/libjvm.so',      # Java 8 (32-bit)
-    'OS:LINUX|ARCH:X86|jre/lib/i386/server/libjvm.so',  # Java 8 (32-bit)
-    'OS:MACOSX|lib/libjli.dylib',                       # Java 12+
-    'OS:MACOSX|lib/jli/libjli.dylib',                   # Java 9-11
-    'OS:MACOSX|jre/lib/jli/libjli.dylib',               # Java 8
-    'OS:WINDOWS|bin\server\jvm.dll',                    # Java 9+
-    'OS:WINDOWS|bin\client\jvm.dll',                    # Java 9+
-    'OS:WINDOWS|jre\bin\server\jvm.dll',                # Java 8
-    'OS:WINDOWS|jre\bin\client\jvm.dll',                # Java 8
-]
-
-# ==============================================================================
-# jvm.classpath
-# ==============================================================================
-# Runtime classpath elements (e.g. JAR files) to pass to Java.
-#
-# These are typically relative paths beneath the application root directory,
-# which is the same directory where the Jaunch launchers and config files reside.
-#
-# The asterisk wildcard symbol (*) is allowed, if you want to match all JAR files,
-# or even all JARs and directories, within a particular directory.
-#
-# The double-asterisk (**) for recursive matching is not yet implemented,
-# but could be done if there is user demand (PRs welcome ;-).
-
-jvm.classpath = [
-    '--class-path|${class-path}',
-    '--jar-path|${jar-path}/*',
-]
-
-# ==============================================================================
-# jvm.max-heap
-# ==============================================================================
-# Maximum amount of memory for the Java heap to consume.
-#
-# In addition to the usual k, m, and g suffixes supported by Java itself for KB,
-# MB, and GB respectively, Jaunch also supports a % suffix.
-#
-# Examples:
-# - For 1567 MB: '1567m'
-# - For 48 GB: '48g'
-# - For 75% of available RAM: '75%'
-# - For 3 GB less than available RAM: '-3g'
-#
-# These will be translated into an appropriate '-Xmx...' argument under the hood.
-#
-# If unset, Java's default will be used (i.e. no -Xmx argument will be injected).
-
-#jvm.max-heap = '50%'
-
-# ==============================================================================
-# jvm.runtime-args
-# ==============================================================================
-# Arguments to pass to the JVM.
-#
-# This is the magic sauce where Jaunch options and other criteria get translated
-# into JVM arguments. See 'jvm.root-paths' above for a thorough explanation.
-
-jvm.runtime-args = [
-    '--headless|-Djava.awt.headless=true',
-    '--headless|-Dapple.awt.UIElement=true',
-    '--heap|-Xmx${heap}',
-    '--ext|-Djava.ext.dirs=${ext}',
-    '--debugger|-agentlib:jdwp=transport=dt_socket,server=y,address=localhost:${debugger}',
-]
-
-# ==============================================================================
-# jvm.main-class
-# ==============================================================================
-# A list of candidate main classes, one of which will get launched.
-#
-# Jaunch evaluates the rules attached to each candidate main class. The first
-# line with matching rules becomes the main class, with subsequent lines ignored.
-#
-# This field is useful if you want to launch a different main class depending on
-# criteria such as OS, CPU architecture, or which options are given on the CLI.
-
-#jvm.main-class = [
-#    '--fizzbuzz|org.fizzbuzz.FizzBuzz',
-#    '--main-class|${main-class}',
-#    'org.fizzbuzz.Main', # default behavior
-#]
-
-# ==============================================================================
-# jvm.main-args
-# ==============================================================================
-# Arguments to pass to the main class on the Java side.
-#
-# This is the other half of the magic sauce, along with jvm.runtime-args above:
-# Options and other criteria get translated into main arguments here.
-# See the 'jvm.root-paths' section above for a thorough explanation.
-
-#jvm.main-args = [
-#    '!--fizz|!--buzz|--mode=number',
-#    '--fizz|!--buzz|--mode=fizz',
-#    '--buzz|!--fizz|--mode=buzz',
-#    '--fizz|--buzz|--mode=fizzbuzz',
-#]

fiji/fiji-linux64/Fiji.app/config/jaunch/python.toml

@@ -1,290 +0,0 @@
-# Shared Jaunch configuration for Python-based programs.
-#
-# See the common.toml file for an introduction to Jaunch configuration.
-
-includes = ['common.toml']
-
-# ==============================================================================
-# Python-specific Jaunch options.
-
-supported-options = [
-    '--python-home=<path>|specify PYTHON_HOME explicitly',
-    '--print-python-home|print path to the selected Python',
-    '--print-python-info|print information about the selected Python',
-]
-
-# ==============================================================================
-# Python-specific modes:
-#
-# * LAUNCH:PYTHON - when set, PYTHON will be included in the directives.
-
-#modes = ['LAUNCH:PYTHON']
-
-# ==============================================================================
-# Python-specific directives:
-#
-# * PYTHON             - Launches the main program using the Python interpreter.
-# * print-python-home  - Print out the path to the chosen Python installation.
-# * print-python-info  - Print out all the details of the chosen Python
-#                        installation, including not only its path, but also
-#                        the libPython path, version, and installed packages.
-
-directives = [
-    'LAUNCH:PYTHON|PYTHON',
-    '--print-python-home|print-python-home,ABORT',
-    '--print-python-info|print-python-info,ABORT',
-]
-
-# ==============================================================================
-# python.enabled
-# ==============================================================================
-# Set this to true to enable searching for and launching with Python.
-
-python.enabled = true
-
-# ==============================================================================
-# python.recognized-args
-# ==============================================================================
-# The list of arguments that Jaunch will recognize as belonging to Python,
-# rather than to `sys.argv` within the Python script itself.
-#
-# These are used to guess, when the minus-minus divider (--) is absent,
-# whether each arg is a Python (runtime) one or a main one.
-#
-# The asterisk wildcard symbol (*) is allowed as a suffix,
-# if you want to match all arguments with a particular prefix.
-#
-# About main arguments: Jaunch's philosophy is to remain agnostic of the options
-# your application supports, rather than trying to constrain them in its configuration
-# and checking them itself. As such, it is your application's responsibility to emit
-# error messages as appropriate if it encounters displeasing arguments.
-#
-# For example, suppose the user invokes:
-#
-#     ./fizzbuzz 1 2 3 4 5 -i
-#
-# Because '-i' is on the python.recognized-args list out of the box,
-# Jaunch will translate this invocation to:
-#
-#     python -i fizzbuzz.py 1 2 3 4 5
-#
-# Even though the Python argument appears after the main arguments. Users can mix
-# and match to their hearts' content, being as sloppy as they want, and Jaunch will
-# sort out the mess. As long as the Python args are on the list here, of course.
-
-python.recognized-args = [
-    '-b', '-bb',
-    '-B',
-    '-c cmd',
-    '-d',
-    '-E',
-    '-?', # --help and -h are reserved for Jaunch
-    '-i',
-    '-I',
-    '-m mod',
-    '-O',
-    '-OO',
-    '-q',
-    '-s',
-    '-S',
-    '-u',
-    '-v',
-    '-V', # --version is reserved for Jaunch
-    '-W arg',
-    '-x',
-    '-X opt',
-    '--check-hash-based-pycs always|default|never',
-]
-
-# ==============================================================================
-# python.root-paths
-# ==============================================================================
-# Paths to check for Python installations.
-#
-# This is a list of directories where Jaunch might hope to find a Python installation.
-# Directories are checked sequentially until one is found that matches all criteria.
-#
-# This is also the first field where we see Jaunch's hints/rules system in action.
-# See the `modes` section of common.toml for an introduction to hints.
-#
-# The Python runtime adds hints based on the Python installation selected:
-#
-# - PYTHON:3.9 if the selected Python installation is version 3.9.
-# - PYTHON:3.9+ if the selected Python installation is version 3.9 or later.
-# - PYTHON:3.10 if the selected Python installation is version 3.10.
-# - PYTHON:3.10+ if the selected Python installation is version 3.10 or later.
-# - and so on.
-#
-# Of course, Python hints will only be set after a Python installation matches,
-# so they won't work here in python.root-paths, nor in python.lib-suffixes.
-# But they can be useful in the python.runtime-args section to ensure Jaunch
-# passes runtime args only to those versions of Python that support them,
-# such as the -P flag which was introduced in Python 3.11.
-#
-# This is also the first field where we see Jaunch's variables in use:
-#
-#     '--python-home|${python-home}'
-#
-# Thanks to the above line, when the user passes '--python-home=/best', the
-# --python-home hint will be set, and the python-home variable will be set to /best.
-# So not only will the line match, but the root path to check will become /best.
-
-python.root-paths = [
-    '--python-home|${python-home}',                                                               # user override (CLI arg)
-    '!--system|${cfg.python-dir}',                                                                # read from <app>.cfg
-    '!--system|${app-dir}/lib/runtime',                                                           # bundled
-    '!--system|${app-dir}/python',                                                                # bundled
-    '!--system|OS:LINUX|ARCH:ARM64|${app-dir}/python/linux-arm64/*',                              # bundled (Linux arm64)
-    '!--system|OS:LINUX|ARCH:X64|${app-dir}/python/linux64/*',                                    # bundled (Linux x86-64)
-    '!--system|OS:LINUX|ARCH:X86|${app-dir}/python/linux32/*',                                    # bundled (Linux x86-32)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/python/macosx-arm64/*/Contents/Home',              # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:ARM64|${app-dir}/python/macosx-arm64/*',                            # bundled (macOS arm64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/python/macosx/*/Contents/Home',                      # bundled (macOS x86-64)
-    '!--system|OS:MACOSX|ARCH:X64|${app-dir}/python/macosx/*',                                    # bundled (macOS x86-64)
-    '!--system|OS:WINDOWS|ARCH:X64|${app-dir}\python\win64\*',                                    # bundled (Windows x86-64)
-    '!--system|OS:WINDOWS|ARCH:X86|${app-dir}\python\win32\*',                                    # bundled (Windows x86-32)
-    '${PYTHON_HOME}',                                                                             # PYTHON_HOME environment variable
-    '${CONDA_PREFIX}',                                                                            # activated Conda/Mamba env
-    'OS:LINUX|/usr/lib/python*/*',                                                                # system (Linux)
-    'OS:LINUX|ARCH:X64|/usr/lib/x86_64-linux-gnu',                                                # system (Linux x86-64)
-    'OS:LINUX|ARCH:X86|/usr/lib/i386-linux-gnu',                                                  # system (Linux x86-32)
-    'OS:MACOSX|${HOMEBREW_PREFIX}/Caskroom/miniforge/base',                                       # miniforge from Homebrew
-    'OS:MACOSX|/opt/homebrew/Caskroom/miniforge/base',                                            # miniforge from Homebrew (arm64 default)
-    'OS:MACOSX|/usr/local/Caskroom/miniforge/base',                                               # miniforge from Homebrew (x86-64 default)
-    'OS:MACOSX|${HOMEBREW_PREFIX}/Cellar/python*/*/Frameworks/Python.framework/Versions/Current', # python from Homebrew
-    'OS:MACOSX|/opt/homebrew/Cellar/python*/*/Frameworks/Python.framework/Versions/Current',      # python from Homebrew (arm64 default)
-    'OS:MACOSX|/usr/local/Cellar/python*/*/Frameworks/Python.framework/Versions/Current',         # python from Homebrew (x86-64 default)
-    'OS:MACOSX|${HOMEBREW_PREFIX}/Cellar/python*/*/Frameworks/Python.framework/Versions/*',       # python from Homebrew
-    'OS:MACOSX|/opt/homebrew/Cellar/python*/*/Frameworks/Python.framework/Versions/*',            # python from Homebrew (arm64 default)
-    'OS:MACOSX|/usr/local/Cellar/python*/*/Frameworks/Python.framework/Versions/*',               # python from Homebrew (x86-64 default)
-    'OS:WINDOWS|${LOCALAPPDATA}\Programs\Python\*',                                               # system (Windows)
-    '${MAMBA_ROOT_PREFIX}/envs/*',                                                                # all Mamba envs
-    '${CONDA_ROOT}/envs/*',                                                                       # all Conda envs
-]
-
-# ==============================================================================
-# Developer aside: Right now, Jaunch does not utilize any programmatic ways
-# to discover Python root directories. But it could! For example, it could
-# invoke `mamba env list` to get a list of installed Conda/Mamba environments.
-#
-# We could invent schema elements for toggling use of such detection approaches.
-# But for now: YAGNI! File an issue or a pull request if you do need it.
-
-# ==============================================================================
-# python.lib-suffixes
-# ==============================================================================
-# List of places within a Python installation to look for the Python library.
-#
-# For example, if the root directory currently being considered is
-# /the-best-python, and the current lib-suffixes line is lib/libpython3.so,
-# then Jaunch will check the path /the-best-python/lib/libpython3.so for the
-# library. If found, we have a winning Python installation!
-
-# TODO: Verify this list for all platforms.
-python.lib-suffixes = [
-    'OS:LINUX|lib/libpython3.so',
-    'OS:LINUX|lib/libpython3.13.so',
-    'OS:LINUX|lib/libpython3.12.so',
-    'OS:LINUX|lib/libpython3.11.so',
-    'OS:LINUX|lib/libpython3.10.so',
-    'OS:LINUX|lib/libpython3.9.so',
-    'OS:LINUX|lib/libpython3.8.so',
-    'OS:LINUX|libpython3.so',
-    'OS:LINUX|libpython3.13.so',
-    'OS:LINUX|libpython3.12.so',
-    'OS:LINUX|libpython3.11.so',
-    'OS:LINUX|libpython3.10.so',
-    'OS:LINUX|libpython3.9.so',
-    'OS:LINUX|libpython3.8.so',
-    'OS:MACOSX|lib/libpython3.dylib',
-    'OS:MACOSX|lib/libpython3.13.dylib',
-    'OS:MACOSX|lib/libpython3.12.dylib',
-    'OS:MACOSX|lib/libpython3.11.dylib',
-    'OS:MACOSX|lib/libpython3.10.dylib',
-    'OS:MACOSX|lib/libpython3.9.dylib',
-    'OS:MACOSX|lib/libpython3.8.dylib',
-    'OS:WINDOWS|python313.dll',
-    'OS:WINDOWS|python312.dll',
-    'OS:WINDOWS|python311.dll',
-    'OS:WINDOWS|python310.dll',
-    'OS:WINDOWS|python39.dll',
-    'OS:WINDOWS|python38.dll',
-    'OS:WINDOWS|python3.dll',
-    'OS:WINDOWS|lib\python313.dll',
-    'OS:WINDOWS|lib\python312.dll',
-    'OS:WINDOWS|lib\python311.dll',
-    'OS:WINDOWS|lib\python310.dll',
-    'OS:WINDOWS|lib\python39.dll',
-    'OS:WINDOWS|lib\python38.dll',
-    'OS:WINDOWS|lib\python3.dll',
-]
-
-# ==============================================================================
-# python.version-min, python.version-max
-# ==============================================================================
-# Acceptable range of Python versions to match.
-#
-# These two fields let you constrain the minimum and maximum Python versions
-# respectively that your application supports. This information will be used when
-# searching the system for appropriate Python installations. If a Python installation
-# is successfully discovered, but then found to be outside these constraints, it is
-# discarded and the search continues.
-#
-# The most common use of these fields is to specify a major.minor version pair
-# (e.g. `python.version-min = '3.9'`), but Jaunch does compare version strings digit by
-# digit, so you could write `python.version-min = '3.8.5' if you need to be specific.
-
-python.version-min = '3.8'
-#python.version-max = '3.12'
-
-# ==============================================================================
-# python.packages
-# ==============================================================================
-# Packages that must be present in the Python installation.
-#
-# TODO The syntax is similar to requirements.txt.
-
-python.packages = []
-
-# ==============================================================================
-# python.runtime-args
-# ==============================================================================
-# Arguments to pass to Python.
-#
-# This is the magic sauce where Jaunch options and other criteria get translated
-# into Python arguments. See 'python.root-paths' above for a thorough explanation.
-
-python.runtime-args = []
-
-# ==============================================================================
-# python.script-path
-# ==============================================================================
-# A list of paths to candidate main scripts, one of which will get launched.
-#
-# Jaunch evaluates the rules attached to each candidate main script. The first
-# line with matching rules becomes the main script, with subsequent lines ignored.
-#
-# This field is useful if you want to launch a different main script depending on
-# criteria such as OS, CPU architecture, or which options are given on the CLI.
-
-#python.script-path = [
-#    '--fizzbuzz|fizzbuzz.py'
-#    '--script-path|${script-path}',
-#    'main.py', # default behavior
-#]
-
-# ==============================================================================
-# python.main-args
-# ==============================================================================
-# Arguments to pass to the main script on the Python side.
-#
-# This is the other half of the magic sauce, along with python.runtime-args above:
-# Options and other criteria get translated into main arguments here.
-# See the 'python.root-paths' section above for a thorough explanation.
-
-#python.main-args = [
-#    '!--fizz|!--buzz|--mode=number',
-#    '--fizz|!--buzz|--mode=fizz',
-#    '--buzz|!--fizz|--mode=buzz',
-#    '--fizz|--buzz|--mode=fizzbuzz',
-#]

fiji/fiji-linux64/Fiji.app/config/jaunch/repl.toml

@@ -1,33 +0,0 @@
-# *** Welcome to the example application configuration file! ***
-#
-# This launcher is built on Jaunch (https://github.com/scijava/jaunch).
-#
-# The contents below define this particular launcher's behavior and features,
-# on top of Jaunch's "sensible default" functionality.
-#
-# See the common.toml file for more details about Jaunch configuration.
-
-jaunch-version = 1
-
-program-name = 'REPL'
-
-includes = ['python.toml', 'jvm.toml']
-
-supported-options = [
-    '--python|Launch the Python REPL',
-    '--jshell|Launch the jshell REPL',
-]
-
-# Launch neither Python nor the JVM by default.
-# Only launch Python when --python flag is given.
-# Only launch the JVM when --jshell flag is given.
-modes = [
-    '--python|LAUNCH:PYTHON',
-    '--jshell|LAUNCH:JVM',
-]
-
-python.runtime-args = ['-i']
-
-jvm.version-min = '9'
-
-jvm.main-class = ['jdk.internal.jshell.tool.JShellToolProvider']

fiji/fiji-linux64/Fiji.app/db.xml.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a026169e863774861c7b6168e199b7beeb8e7fcd1dfdcd32df5571f2d66c031b
-size 365230

fiji/fiji-linux64/Fiji.app/fiji

@@ -1,47 +0,0 @@
-#!/bin/sh
-
-# This shell script is a shortcut for launching the application
-# without regard for the underlying operating system (Linux, macOS,
-# or Windows via Git Bash) or architecture (x86-64 or arm64).
-
-dir=$(dirname "$0")
-name=$(basename "$0")
-name=${name%.sh}
-
-die() { echo "$*" >&2; exit 1; }
-
-# Glean CPU architecture.
-arch=$(uname -m 2>/dev/null)
-case "$arch" in
-  arm64|aarch64) arch=arm64 ;;
-  x86_64|amd64) arch=x64 ;;
-  *) die "Unsupported CPU architecture: $arch" ;;
-esac
-
-# Glean operating system.
-os=$(uname -s 2>/dev/null)
-case "$os" in
-  Linux) launcher="$dir/$name-linux-$arch" ;;
-  Darwin) launcher="$dir/$name-macos-$arch" ;;
-  MINGW*|MSYS*) launcher="$dir/$name-windows-$arch" ;;
-  *) die "Unsupported operating system: $os" ;;
-esac
-
-# Launch with the appropriate executable.
-test -e "$launcher" || {
-  # On macOS, try harder to locate the appropriate executable.
-  case "$os" in
-    Darwin)
-      # Toplevel launcher or symlink not present; look in .app bundles.
-      for macAppDir in "$dir"/*.app; do
-        candidate="$macAppDir"/Contents/MacOS/"$name-macos-$arch"
-        if [ -e "$candidate" ]; then
-          launcher="$candidate"
-          break
-        fi
-      done
-      ;;
-  esac
-  test -e "$launcher" || die "Launcher not available: $launcher"
-}
-"$launcher" "$@"

fiji/fiji-linux64/Fiji.app/fiji.bat

@@ -1,32 +0,0 @@
-@echo off
-
-rem # This batch file is a shortcut for launching the application
-rem # without regard for the underlying architecture (x86-64 or arm64).
-rem # It also forces a new console to be allocated if the parent process
-rem # does not already have one, which is especially useful for
-rem # executables compiled in GUI mode rather than console mode, so that:
-rem #
-rem # 1) the shell prompt blocks until the program completes; and
-rem #
-rem # 2) the console's standard input is all fed to the launched program,
-rem #    rather than haphazardly split between it and the parent shell.
-rem #
-rem # As an alternative to using this batch file wrapper, GUI executables
-rem # can be launched in blocking mode from an existing PowerShell via:
-rem #
-rem #     Start-Process -Wait .\launcher-windows-x64.exe
-rem #
-rem # or from an existing Command Prompt via:
-rem #
-rem #     start /wait launcher-windows-x64.exe
-rem #
-rem # Where `launcher-windows-x64.exe` is the GUI executable to run.
-
-if "%PROCESSOR_ARCHITECTURE%" == "AMD64" (
-    @"%~dp0%~n0-windows-x64.exe" %*
-) else if "%PROCESSOR_ARCHITECTURE%" == "ARM64" (
-    @"%~dp0%~n0-windows-arm64.exe" %*
-) else (
-    echo Unsupported CPU architecture: %PROCESSOR_ARCHITECTURE%
-    exit /b 1
-)

fiji/fiji-linux64/Fiji.app/images/about/about1.tif.txt

@@ -1,4 +0,0 @@
-attribution This image courtesy of Tom Deerinck
-attribution via a Creative Commons license
-fontsize 45
-color 255 255 0

fiji/fiji-linux64/Fiji.app/images/about/about2.tif.txt

@@ -1,4 +0,0 @@
-attribution This image courtesy of Spike Walker
-attribution via a Creative Commons license
-fontsize 50
-color 255 140 0

fiji/fiji-linux64/Fiji.app/images/about/about3.tif.txt

@@ -1,4 +0,0 @@
-attribution This image from ESO/J. Emerson/VISTA
-attribution Cambridge Astronomical Survey Unit
-fontsize 40
-color 255 255 0

fiji/fiji-linux64/Fiji.app/images/about/about4.tif.txt

@@ -1,3 +0,0 @@
-attribution This image courtesy of Hank L. Oppenheimer
-attribution via a Creative Commons license
-color 255 255 0

fiji/fiji-linux64/Fiji.app/images/about/about5.tif.txt

@@ -1,4 +0,0 @@
-attribution This image courtesy of Annie Cavanagh
-attribution via a Creative Commons license
-fonstsize 30
-color 0 255 0

fiji/fiji-linux64/Fiji.app/jars/FilamentDetector-2.0.1.jar

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:5d9189b2b3934f07e6f631fb4b9a010b6b455dfd75a27dce6b10abae9014fc25
-size 1580696

fiji/fiji-linux64/Fiji.app/jars/JWlz-1.4.0.jar

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:0662cfe9600c24cbef591e17f0bfbbbebbae8b0e8d83098735454a999166410f
-size 117846

fiji/fiji-linux64/Fiji.app/jars/Kappa-2.0.0.jar

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-version https://git-lfs.github.com/spec/v1
-oid sha256:735492fc23f35b1db30b40bfc8c895b9002eec780824d5d35ab872f74265f644
-size 273210

fiji/fiji-linux64/Fiji.app/jars/ST4-4.3.4.jar

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f927ac384c46d749f8b5ec68972a53aed21e00313509299616edb73bfa15ff33
-size 251081

fiji/fiji-linux64/Fiji.app/jars/T2-NIT-1.1.4.jar

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-version https://git-lfs.github.com/spec/v1
-oid sha256:80efd205a614aa49950b370dbac2b6156f10acf9e22ff32e94c626cc515e6da8
-size 1351980

fiji/fiji-linux64/Fiji.app/jars/TrackMate-7.14.0.jar

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-version https://git-lfs.github.com/spec/v1
-oid sha256:dcd5426ddc4f4bd159bb722b3b4fea977dfbb146c670b4fc53dec0eb4a14a87f
-size 1642752

fiji/fiji-linux64/Fiji.app/jars/VIB-lib-2.2.0.jar

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-version https://git-lfs.github.com/spec/v1
-oid sha256:5c1a9f55c910b764b328c0468feda27b51f2ef4feca559154f741f698afd26d5
-size 636833

fiji/fiji-linux64/Fiji.app/jars/aircompressor-0.21.jar

@@ -1,3 +0,0 @@
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