Fix broken links to ImageJ2 repository resources

The repository moved from imagej/imagej to imagej/imagej2;
meanwhile, the imagej/imagej1 repo moved to imagej/ImageJ.

Author: ctrueden

_pages/develop/project-management.md

@@ -148,7 +148,7 @@ Issues and milestones are public-facing entities, yet their content can be highl
         <p>to plan development timelines</p>
       </td>
       <td>
-        <p>Use future <a href="https://guides.github.com/features/issues/#filtering">milestones</a> (e.g., <a href="https://github.com/imagej/imagej/milestones">imagej</a>, <a href="https://github.com/scifio/scifio/milestones">scifio</a>).</p>
+        <p>Use future <a href="https://guides.github.com/features/issues/#filtering">milestones</a> (e.g., <a href="https://github.com/imagej/imagej2/milestones">imagej2</a>, <a href="https://github.com/scifio/scifio/milestones">scifio</a>).</p>
       </td>
     </tr>
     <tr>
@@ -157,7 +157,7 @@ Issues and milestones are public-facing entities, yet their content can be highl
         <p>to report completed features</p>
       </td>
       <td>
-        <p>Use completed <a href="https://guides.github.com/features/issues/#filtering">milestones</a> (e.g., <a href="https://github.com/imagej/imagej/milestones?state=closed">imagej</a>, <a href="https://github.com/scifio/scifio/milestones?state=closed">scifio</a>).</p>
+        <p>Use completed <a href="https://guides.github.com/features/issues/#filtering">milestones</a> (e.g., <a href="https://github.com/imagej/imagej2/milestones?state=closed">imagej2</a>, <a href="https://github.com/scifio/scifio/milestones?state=closed">scifio</a>).</p>
       </td>
     </tr>
   </tbody>

_pages/discuss/bugs.md

@@ -11,7 +11,7 @@ Please report bugs via the [Image.sc Forum](https://forum.image.sc/):
 - Include a [minimal working example](#bug-reporting-best-practices) illustrating the issue.
 - If you know who is responsible for maintaining the affected part of the software, please `@mention` them.
 
-Or if you have a GitHub account, please feel welcome to report issues [on GitHub](https://github.com/imagej/imagej/issues) instead.
+Or if you have a GitHub account, please feel welcome to report issues on GitHub in the [ImageJ](https://github.com/imagej/ImageJ/issues),[ImageJ2](https://github.com/imagej/imagej2/issues), [Fiji](https://github.com/fiji/fiji/issues) repositories.
 
 Thank you! 😁
 

_pages/editing/statbox.md

@@ -121,7 +121,7 @@ Several fields have URL/label pairs for better control over display text:
 
 ```yaml
 ---
-release-url: https://github.com/imagej/imagej/releases/tag/v2.14.0
+release-url: https://github.com/imagej/imagej2/releases/tag/v2.14.0
 release-version: "2.14.0"
 license-url: /licensing/bsd
 license-label: "BSD-2"

_pages/licensing/index.md

@@ -127,7 +127,7 @@ The following table summarizes the dominant license of each project's components
     <tr>
       <td><img src="/media/icons/imagej2.png" width="48"></td>
       <th><a href="/software/imagej2">ImageJ2</a></th>
-      <td><a href="https://github.com/imagej/imagej/blob/-/LICENSE.txt">License</a></td>
+      <td><a href="https://github.com/imagej/imagej2/blob/-/LICENSE.txt">License</a></td>
     </tr>
     <tr>
       <td><img src="/media/icons/scifio.png" width="48"></td>

_pages/news/2011-10-07-unit-tests-for-imagej-1-45.md

@@ -6,7 +6,7 @@ When we launched the [ImageJ2](/software/imagej2) project, we began by writing m
 
 Originally, the tests were designed to run against a modified version of IJ1 that we were developing to facilitate integration with IJ2. However, as development continued, we settled on a design that achieves maximum [compatibility](/libs/imagej-legacy) by embedding IJ1 as-is within IJ2, enabling IJ1 to continue developing in parallel with IJ2. We eliminated the modified version of IJ1, with only the unit tests being retained. Unfortunately, we did not finish fully transitioning the tests, and they were not compiling against stock versions of IJ1.
 
-As of now, we have fixed up the tests to compile ([r4092](https://github.com/imagej/imagej/commit/9fc9ac6599c279bc83eb0a62d922f34517c47e37)) and run ([r4096](https://github.com/imagej/imagej/commit/b51494bb19c094b4430d3936a5e30383c722b35a), [r4098](https://github.com/imagej/imagej/commit/d1d4ffd94096a0843e751533d909513faaccb7c3)) against stock versions of ImageJ v1.44 and later, and posted [instructions for running them](/develop/ij1-unit-tests).
+As of now, we have fixed up the tests to compile ([r4092](https://github.com/imagej/imagej2/commit/9fc9ac6599c279bc83eb0a62d922f34517c47e37)) and run ([r4096](https://github.com/imagej/imagej2/commit/b51494bb19c094b4430d3936a5e30383c722b35a), [r4098](https://github.com/imagej/imagej2/commit/d1d4ffd94096a0843e751533d909513faaccb7c3)) against stock versions of ImageJ v1.44 and later, and posted [instructions for running them](/develop/ij1-unit-tests).
 
 We then ran the tests against all the 1.45 development versions. The results are below.
 

_pages/news/2012-03-09-auto-synchronizing-repositories.md

@@ -14,7 +14,7 @@ Alas, a solution is nigh!
 
 We solved exactly those problems in the ImageJ project. There is a [Jenkins job](http://jenkins.imagej.net/view/Synchronizers/job/ImageJ-synchronizer/) to synchronize the ImageJ repositories with each other, using {% include github org='scijava' repo='scijava-scripts' branch='master' path='git-synchronizer.sh' label='this script' %}. Sadly the script is a little more complex than I hoped, but it does the job reliably and to be honest, it is a little more tricky than I first thought: when there are updates from only one of the repositories, they should be forced. However, there might be contradicting updates in which case nothing may be forced. Of course, such a script—especially when it is a little more complex than the author hoped—also has to take precautions not to be overzealous in corner-cases the author might have not thought about. That is the reason why it makes extra-sure to look for updates it might have missed in earlier rounds and does **not** force those updates. [Jenkins](/develop/jenkins) executes this job every 5 minutes which is why it is very important that the much faster `git://` protocol is used for fetching the branches instead of the slower ssh-based protocol used for pushing.
 
-As for the git-svn mirror, we have a Jenkins job that too. It is driven by a—thankfully quite simple—[script](https://github.com/imagej/imagej/blob/9227a1048426dc2c1b312be4e8a80c1b726a04ce%5E/bin/jenkins-git-job.sh). This script makes sure that the remote information is set up such that all branches in `refs/remotes/` (i.e. the ones maintained by git-svn) are pushed into the `refs/heads/svn/` namespace. Jenkins polls the Subversion repository and only runs the job when new commits are available.
+As for the git-svn mirror, we have a Jenkins job that too. It is driven by a—thankfully quite simple—[script](https://github.com/imagej/imagej2/blob/9227a1048426dc2c1b312be4e8a80c1b726a04ce%5E/bin/jenkins-git-job.sh). This script makes sure that the remote information is set up such that all branches in `refs/remotes/` (i.e. the ones maintained by git-svn) are pushed into the `refs/heads/svn/` namespace. Jenkins polls the Subversion repository and only runs the job when new commits are available.
 
 Both jobs (and likewise the siblings of the ImageJ synchronizer used to synchronize the {% include github repo='imglib' label='ImgLib2' %} and {% include github repo='fiji' label='Fiji' %} repositories) proved quite useful and stable in our development.
 

_pages/news/2012-04-09-imagej-v2-0-0-beta1.md

@@ -99,9 +99,9 @@ For more about the Maven artifacts associated with the release, see [this techni
 
 ## The ImageJ2 logo
 
-{% include img align="left" src="/media/news/imagej2-icon-v1.png" width="128px" alt="ImageJ2 icon" %} You may have noticed the [new microscope logo](https://github.com/imagej/imagej/blob/-/logo/imagej2-v1/imagej.png) for ImageJ2. This image is not the final logo. The plan is to solicit community submissions for a logo, then vote on the mailing list to decide. The current logo is a placeholder image being used during the beta phase of development.
+{% include img align="left" src="/media/news/imagej2-icon-v1.png" width="128px" alt="ImageJ2 icon" %} You may have noticed the [new microscope logo](https://github.com/imagej/imagej2/blob/-/logo/imagej2-v1/imagej.png) for ImageJ2. This image is not the final logo. The plan is to solicit community submissions for a logo, then vote on the mailing list to decide. The current logo is a placeholder image being used during the beta phase of development.
 
-For more details on the logo including source and design credits, see [this readme](https://github.com/imagej/imagej/blob/8a2b33226b7eb6d1ec62a708978e092a736638e5/logo/readme.txt).
+For more details on the logo including source and design credits, see [this readme](https://github.com/imagej/imagej2/blob/8a2b33226b7eb6d1ec62a708978e092a736638e5/logo/readme.txt).
 
 ## Roadmap and future directions
 

_pages/news/2012-10-19-imagej-v2-0-0-beta5.md

@@ -18,32 +18,32 @@ Development of this release of ImageJ focused on the addition of [scripting](/sc
 
 {% include img align="right" src="/media/news/hello-world-script.png" caption="Written and executed from the Script Editor!" width="362px" %}
 
--   New script editor! This is the artist formerly known as the [Fiji Script Editor](/scripting/script-editor), much refurbished and with a shiny new rewrite of the scripting infrastructure. It even comes with basic support for Maven projects. \[[commit](https://github.com/imagej/imagej/commit/7e0cea20311f86cacce8afa2a6bcea612e180b47)\]
--   There is now a Noise Reduction menu that supports a few noise reduction methods. \[[code](https://github.com/imagej/imagej/tree/v2.0.0-beta5/core/commands/data/src/main/java/imagej/core/commands/assign/noisereduce)\]
+-   New script editor! This is the artist formerly known as the [Fiji Script Editor](/scripting/script-editor), much refurbished and with a shiny new rewrite of the scripting infrastructure. It even comes with basic support for Maven projects. \[[commit](https://github.com/imagej/imagej2/commit/7e0cea20311f86cacce8afa2a6bcea612e180b47)\]
+-   There is now a Noise Reduction menu that supports a few noise reduction methods. \[[code](https://github.com/imagej/imagej2/tree/v2.0.0-beta5/core/commands/data/src/main/java/imagej/core/commands/assign/noisereduce)\]
 -   The Command Finder now has a full set of sortable columns. \[[#1483](http://trac.imagej.net/ticket/1483)\]
--   There is now a "Show LUT As Table" command. \[[commit](https://github.com/imagej/imagej/commit/838b00cc3e1291145c8782a1c6343d861b079f89)\]
+-   There is now a "Show LUT As Table" command. \[[commit](https://github.com/imagej/imagej2/commit/838b00cc3e1291145c8782a1c6343d861b079f89)\]
 -   The current foreground and background colors are displayed on the toolbar.
 -   Creating grayscale images from multichannel data is now easier.
 
 ### Architecture changes
 
 -   **Redesigned scripting framework.** A scripting language is now a type of plugin, meaning anyone can create and register their own scripting language within ImageJ. \[[#12](http://trac.imagej.net/ticket/12)\]
 -   **Results tables**. They can be declared as outputs of commands, and will be automatically displayed in a new table window. \[[#1250](http://trac.imagej.net/ticket/1250)\]
--   **Statistics service.** The statistics service simplifies the measurement of statistics from a set of data. There is an example (see below) which shows how it can be used. \[[commit](https://github.com/imagej/imagej/commit/fc5e1434658b1ec562d0f816ff6244195de1c12a)\]
+-   **Statistics service.** The statistics service simplifies the measurement of statistics from a set of data. There is an example (see below) which shows how it can be used. \[[commit](https://github.com/imagej/imagej2/commit/fc5e1434658b1ec562d0f816ff6244195de1c12a)\]
 -   **Improvements to Imglib2 OPS.** \[[#1511](http://trac.imagej.net/ticket/1511)\]
--   **Efficient Collections-based primitive array lists.** The Java standard library does not have a performant way to wrap primitive types—such as `int` and `double`—in `ArrayList`s. We now have performant implementations of growable primitive-type arrays in *imagej.util.IntArray* and friends. These classes were added to support results tables, but their utility goes beyond just results tables. \[[commit](https://github.com/imagej/imagej/commit/0789b57d8d3622ea09e4b677b1b0153367eed5b4)\]
--   **Better detection of the ImageJ base directory.** This fixes a bug when using ImageJ2 from within KNIME. \[[commit](https://github.com/imagej/imagej/commit/66b4e29ede811ad14ebd911ee9f3b0d26935c195)\]
--   **Better naming of displays.** \[[commit](https://github.com/imagej/imagej/commit/6f8576e8082ab6b4c8a778e6c3e927265d34295b)\]
--   **More consistent display viewer package hierarchies.** \[[commit](https://github.com/imagej/imagej/commit/687f6035842d7e9af512f90c8fddc1af99eb30a5)\]
--   **Plugin index bugfixes.** \[[commit](https://github.com/imagej/imagej/commit/6253b9a537a4598f3aca1d5e098aadec10bb4ba1)\]
+-   **Efficient Collections-based primitive array lists.** The Java standard library does not have a performant way to wrap primitive types—such as `int` and `double`—in `ArrayList`s. We now have performant implementations of growable primitive-type arrays in *imagej.util.IntArray* and friends. These classes were added to support results tables, but their utility goes beyond just results tables. \[[commit](https://github.com/imagej/imagej2/commit/0789b57d8d3622ea09e4b677b1b0153367eed5b4)\]
+-   **Better detection of the ImageJ base directory.** This fixes a bug when using ImageJ2 from within KNIME. \[[commit](https://github.com/imagej/imagej2/commit/66b4e29ede811ad14ebd911ee9f3b0d26935c195)\]
+-   **Better naming of displays.** \[[commit](https://github.com/imagej/imagej2/commit/6f8576e8082ab6b4c8a778e6c3e927265d34295b)\]
+-   **More consistent display viewer package hierarchies.** \[[commit](https://github.com/imagej/imagej2/commit/687f6035842d7e9af512f90c8fddc1af99eb30a5)\]
+-   **Plugin index bugfixes.** \[[commit](https://github.com/imagej/imagej2/commit/6253b9a537a4598f3aca1d5e098aadec10bb4ba1)\]
 
 ### Improved help
 
 Some command dialogs now have Help buttons that load a wiki page describing the command. Such commands include the Overlay Manager, the ImageJ 1.x Compatibilty Mode options, the {% include bc path="Process | Math | Equation" %} command, and the PointSet Demo command. This kind of immediate help via the wiki will be utilized more going forward.
 
 ### Examples for developers
 
-We have continued to flesh out example code for developers. In this release there is an example of [how to use the new StatisticsService](https://github.com/imagej/imagej/blob/v2.0.0-beta5/core/commands/debug/src/main/java/imagej/core/commands/debug/StatisticsDemo.java), an example showing [how plugin parameters are assigned](https://github.com/imagej/imagej/blob/v2.0.0-beta5/core/commands/debug/src/main/java/imagej/core/commands/debug/ParamAssignOrder.java), and an example in Imglib2 on [how to use OPS to combine images](https://github.com/imagej/imglib/blob/v2.0.0-beta5/imglib2/ops/src/main/java/net/imglib2/ops/img/ImageCombiner.java). We have also added a new [tutorial on creating a custom preprocessor plugin](https://github.com/imagej/tutorials/tree/8e63ef56384505612cd2b1abb231b12509117d7c/custom-preprocessor-plugin).
+We have continued to flesh out example code for developers. In this release there is an example of [how to use the new StatisticsService](https://github.com/imagej/imagej2/blob/v2.0.0-beta5/core/commands/debug/src/main/java/imagej/core/commands/debug/StatisticsDemo.java), an example showing [how plugin parameters are assigned](https://github.com/imagej/imagej2/blob/v2.0.0-beta5/core/commands/debug/src/main/java/imagej/core/commands/debug/ParamAssignOrder.java), and an example in Imglib2 on [how to use OPS to combine images](https://github.com/imagej/imglib/blob/v2.0.0-beta5/imglib2/ops/src/main/java/net/imglib2/ops/img/ImageCombiner.java). We have also added a new [tutorial on creating a custom preprocessor plugin](https://github.com/imagej/tutorials/tree/8e63ef56384505612cd2b1abb231b12509117d7c/custom-preprocessor-plugin).
 
 ### Compatibility