Convert direct wiki links to local

Author: Tom-Willemsen

doc/IOCs.md

@@ -17,7 +17,7 @@ Remember, EPICS is a collaboration! Why create an IOC when you can just use one
 
 Building a new IOC? Before you get started, take a look at the relevant [instrument page](https://github.com/ISISComputingGroup/IBEX/wiki) to see if there's any useful information for the device you're about to write an IOC for. Otherwise, let's get going. If you have problems see [See IOC and device Troubleshooting](iocs/Troubleshooting).
 
-There are two sorts of IOCs, EPICs and pycaspy. For EPICs type see the automatic creation below for pycaspy see the [pycaspy ioc](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/ioc-pcaspy).
+There are two sorts of IOCs, EPICs and pycaspy. For EPICs type see the automatic creation below for pycaspy see the [pycaspy ioc](/iocs/creation/ioc-pcaspy).
 
 Need more than 1 IOC? See [IOC Duplication](iocs/creation/Duplicating-IOCs)
 

doc/Providing-Support.md

@@ -108,7 +108,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
   <summary>I can't see the dataweb for {instrument}</summary>
 
   1. Check whether or not you can see that dataweb, and how extensive the failure is (one instrument, many, all) (TODO: Find out the solution for this, is it always restart the dataweb server/JSON_BOURNE?
-  2. Try the troubleshooting section on the [dataweb](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Web-Dashboard#troubleshooting)
+  2. Try the troubleshooting section on the [dataweb](#webdashboard_troubleshooting)
   3. If this doesn't work try restarting ndaextweb3
 
 </details>
@@ -119,7 +119,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
   1. I can't talk to device/my blocks are showing as disconnected/IOC isn't working
       - Check that the IOC is running
       - Check that the device is turned on
-      - Check if your problem is already listed on the [device/ioc wiki pages](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Specific-Device-IOC).
+      - Check if your problem is already listed on the [device/ioc wiki pages](Specific-IOCs).
       - If the device is a DAQmx one, look at it in MAX, and perform a self-test
       - Device not responding
           * Stop the IOC (or VI) and try to connect via a more direct route, e.g. Putty
@@ -153,7 +153,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
      - Verify that the device expected on that port is the device connected on that port
      - Treat it as a device that is unable to interact
      - Check the error logs (either through the log interface in the GUI, the console logs, or other appropriate method)
-     - Verify that the behaviour you're seeing is not a known quirk of the device. These quirks are often detailed on the [device/ioc wiki pages](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Specific-Device-IOC)
+     - Verify that the behaviour you're seeing is not a known quirk of the device. These quirks are often detailed on the [device/ioc wiki pages](Specific-IOCs)
 
 </details>
 
@@ -170,7 +170,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
 
   1. There are a few things that have services which run, especially the databases, and it is possible after a crash/other restart that these don't start up again, starting task manager as an administrator should allow you to start the service in question
   1. If it is not one of our services (e.g. swipe systems, ERA), we cannot resolve the issue, escalate as appropriate (TODO: Make sure the different escalation methods are documented)
-  1. If the MCR news service isn't working, then so long as there is space, restarting our [webserver](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Webserver) may help.
+  1. If the MCR news service isn't working, then so long as there is space, restarting our [webserver](/systems/Webserver) may help.
 
 </details>
 

doc/Script-Generator.md

@@ -22,8 +22,9 @@ script_generator/*
 | Standalone app build directories | `base/uk.ac.isis.scriptgenerator/*` |
 
 ## Eclipse build
-To build and run the app through eclipse, the script generator product is found in `base\uk.ac.stfc.isis.scriptgenerator.client.product`. The instructions for setting up eclipse and loading the target platform (necessary for the script generator) are found in the instructions for the [main IBEX GUI setup](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Building-the-GUI)
+To build and run the app through eclipse, the script generator product is found in `base\uk.ac.stfc.isis.scriptgenerator.client.product`. The instructions for setting up eclipse and loading the target platform (necessary for the script generator) are found in the instructions for the [main IBEX GUI setup](/client/getting_started/Building-the-GUI)
 
+{#scriptgenerator_enable_perspective}
 ### Adding the perspective into the client
 Currently the script generator perspective is not shown or selectable in the main IBEX GUI. It can be re-added by selecting `Preferences > Select Visible Perspectives` from the IBEX Main Menu.
 
@@ -35,7 +36,7 @@ There is a Jenkins pipeline which will build the script generator with every new
 
 ## Data structures in the GUI
 
-Each 'action', or step in a script is represented in the GUI as a row. Each cell contains one parameter for an action, which the users change to define their experiment. A complete row of defined parameters should be enough information to run the action once (see [Script Generator High-Level Design](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Script-generator-high-level-design#the-action-class))
+Each 'action', or step in a script is represented in the GUI as a row. Each cell contains one parameter for an action, which the users change to define their experiment. A complete row of defined parameters should be enough information to run the action once (see [Script Generator High-Level Design](#scriptgenerator_script_definition))
 
 ![](scriptgen.png)
 
@@ -44,7 +45,7 @@ The parameter values are stored as strings in the underlying action. These strin
 To change the type of action represented in the table, the singleton drops the current table and replaces it with a new one constructed using the new action type.
 
 ## Importing user-supplied script definitions
-The `ScriptDefinitions` are supplied by instrument scientists in [this form](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Script-generator-high-level-design#the-actiondefinition-class). All the python modules containing an `ScriptDefinition` in a subdirectory are imported and stored in a `ScriptDefinitionWrapper` class. Using an instrument scientist supplied `ScriptDefinition`, a `ScriptDefinitionWrapper` class is created containing the `ScriptDefinition` with helper methods like `getParameters` and `parametersValid` to expose the parameters used in the action and their validation. These `ScriptDefinitionWrapper` classes are collected by the `ScriptDefinitionsWrapper`, which is then passed through the py4j interface to the GUI code.
+The `ScriptDefinitions` are supplied by instrument scientists in [this form](#scriptgenerator_script_definition). All the python modules containing an `ScriptDefinition` in a subdirectory are imported and stored in a `ScriptDefinitionWrapper` class. Using an instrument scientist supplied `ScriptDefinition`, a `ScriptDefinitionWrapper` class is created containing the `ScriptDefinition` with helper methods like `getParameters` and `parametersValid` to expose the parameters used in the action and their validation. These `ScriptDefinitionWrapper` classes are collected by the `ScriptDefinitionsWrapper`, which is then passed through the py4j interface to the GUI code.
 
 On startup of the script generator, the latest versions of the Script Definitions are pulled from [this repository](https://github.com/ISISComputingGroup/ScriptDefinitions). The default location for this repository is in `path_to_script_generator\script_definitions` but can be changed in the `plugin_customisation.ini`. If this directory does not contain the ScriptDefinitions repository on script generator startup, a clone is attempted. If a clone of the ScriptDefintions repository failed from github, a clone is made from a `git bundle` form of the repository, which is shipped with the script generator and is created when the script generator is built.
 
@@ -162,7 +163,7 @@ The script definitions are stored in `c:\instrument\settings\ibex_script_generat
 
 ## Dynamic Scripting
 
-[See here](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/IBEX-Script-Generator-Dynamic-Scripting)
+[See here](script_generator/IBEX-Script-Generator-Dynamic-Scripting)
 
 ## Interested instruments/groups
 

doc/client/GUI-Troubleshooting.md

@@ -85,7 +85,7 @@ You may have built with Java 11 but are running with Java 8 make sure the path i
 You can verify that you are using the correct java version by running `java -version` in a command prompt. It should return java 11 in a non-EPICS terminal, or java 8 in an epics terminal (note, you cannot launch the GUI from an EPICS terminal). If it returns the incorrect version, you can add the correct version to your PATH.
 
 ## File set from project ... has no valid check configuration.
-Try [setting up the checkstyle](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Checkstyle-setup).
+Try [setting up the checkstyle](eclipse/Checkstyle-setup).
 
 ## GUI claims another instance is running upon start (but there isn't)
 Navigate to: `C:/Users/<username>/AppData/Local/IBEX` and delete the file "instance.txt"

doc/client/eclipse/Common-Eclipse-Issues.md

@@ -122,7 +122,7 @@ Sometimes when you check out a new branch in the ibex GUI repository, you won't
 
 1. In Eclipse, remove all the projects from the workspace and close Eclipse.
 1. Then, while checked out to the branch you want to see the changes on, perform a `git clean -fdx && git reset HEAD --hard` to reset the git repository. This will remove any changes you have made to the branch.
-1. Restart Eclipse and repeat the steps to get the GUI working from [Building the GUI](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Building-the-GUI).
+1. Restart Eclipse and repeat the steps to get the GUI working from [Building the GUI](../getting_started/Building-the-GUI).
 
 ## Build fails with `[ERROR] Failed to resolve target definition ... targetplatform.target: Could not find "org.eclipse.e4.tools.spies.feature.feature.group..." in the repositories of the current location`
 

doc/client/getting_started/Building-the-GUI.md

@@ -41,7 +41,7 @@ IBEX should now build but there will probably be some errors. You can clear them
 
 **Important Notes:** 
 * you will need JDK 21 installed to launch the IBEX GUI successfully.
-* you should also [set up the checkstyle](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Checkstyle-setup), do it sooner than later as it may prevent potential errors
+* you should also [set up the checkstyle](../eclipse/Checkstyle-setup), do it sooner than later as it may prevent potential errors
 
 ### If you see a “Plugin execution not covered by lifecycle configuration” error
 1. From the menu bar choose: Window->Preferences
@@ -82,7 +82,7 @@ Sometimes eclipse will tell you that you have errors when you open it. The follo
 - Refresh, clean and build all projects. Select all projects, press F5 to refresh, then go to `Project -> Clean` to clean all projects.
 - Go to `Run -> Run Configurations -> Plugins` and press "Add required plugins". You can now validate/apply your choice.
 - In `uk.ac.stfc.isis.ibex.targetplatform`, open `uk.ac.stfc.isis.ibex.targetplatform.target` and click "set as target platform". 
-- If you have done all these steps and it still doesn't work, there is more troubleshooting information [here](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Common-Eclipse-Issues).
+- If you have done all these steps and it still doesn't work, there is more troubleshooting information [here](../eclipse/Common-Eclipse-Issues).
 - If all else fails, delete all the projects from eclipse's workspace and reimport them.
 
 Eclipse can automatically set the Java standard for some projects to `1.8`. If you are seeing errors such as `var cannot be assigned to a type` on certain projects, navigate to the project in the explorer, then right-click and choose Properties->Java Compiler->Configure Workspace Settings, and then set the required Java standard to `11`.
@@ -91,4 +91,4 @@ If you have a lot of errors make sure that `-Djdk.util.zip.disableZip64ExtraFiel
 
 ## Further Troubleshooting ##
 
-Additional support can be found [here](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/GUI-Troubleshooting).
+Additional support can be found [here](../GUI-Troubleshooting).

doc/client/getting_started/Maven-and-Tycho.md

@@ -366,7 +366,3 @@ In IBEX we define a separate project called `uk.ac.stfc.isis.ibex.client.product
 ```
 
 The key area is the materialize-products section, this tells Tycho to actually create the product. Without this the build runs and checks everything is okay, but does not produce an executable.
-
-## How to add a new plugin to the Maven build ##
-
-https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Adding-a-Plugin-or-Feature-to-Maven-Build

doc/client/misc/Embedding-JavaFX-views-into-IBEX.md

@@ -8,7 +8,7 @@ In order to be able to embed JavaFX views, the efxclipse compatibility layer mus
 
 ### Patching Java to include JavaFX support
 
-To enable JavaFX support on a java installation, it must be patched with the JavaFX overlay. See https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Upgrade-Java#additional-steps for details of how to do this. 
+To enable JavaFX support on a java installation, it must be patched with the JavaFX overlay. See [here](/deployment/deploy/Upgrade-Java) for details of how to do this. 
 
 If you don't do this, you will get an error of the form:
 

doc/client/opis/OPI-Creation.md

@@ -25,8 +25,6 @@ In order to promote consistency in look and feel between different OPIs, we have
 
 Please also make sure your OPI works well for colour blind users, following [these guidelines](../misc/Designing-for-Colour-Blindness).
 
-If you are converting an existing OPI from the old to the new style, be aware of [these tips and gotchas](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Converting-OPI-to-New-Style-Tips-and-Gotchas).
-
 There is a script called `check_opi_format.py` in `C:\Instrument\Dev\ibex_gui\base\uk.ac.stfc.isis.ibex.opis` that can help you check certain aspects of a new OPI. This script does not replace checking the OPI visually, but should help catch some style errors in OPIs. This will iterate over all OPIs in the `C:\Instrument\Dev\ibex_gui\base\uk.ac.stfc.isis.ibex.opis\resources` directory, and write logs to the `C:\Instrument\Dev\ibex_gui\base\uk.ac.stfc.isis.ibex.opis\check_OPI_format_logs` directory by default. Other behaviours are described below:
 
 Usage:

doc/client/testing/Adding-Unit-Tests.md

@@ -1,6 +1,6 @@
 # Adding tests
 
-For more detailed information see [an_introduction_to_unit_testing.rst](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/An-Introduction-to-Unit-Testing).
+For more detailed information see [an_introduction_to_unit_testing.rst](An-Introduction-to-Unit-Testing).
 
 It is relatively simple to add unit tests for a plug-in in such a way that maven can run them as part of the build.
 
@@ -29,7 +29,7 @@ Here are the steps required in Eclipse:
 * Add tests to the class
     * Add org.junit and org.mockito (if required) to the 'Required Plug-ins', under the Dependencies tab for the manifest
 
-* Add the test plug-in to the Maven build by [following these steps](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Adding-a-Plugin-or-Feature-to-Maven-Build)
+* Add the test plug-in to the Maven build by [following these steps](../coding/Adding-a-Plugin-or-Feature-to-Maven-Build)
 
 * Running the Maven build should now also run the tests
 

doc/client/testing/System-Testing-with-Squish-BDD.md

@@ -49,7 +49,7 @@ Now that you have your feature, scenario and steps laid out it's time to write t
 
 To add the steps you want you can either code them directly by writing a test step function or you can record it. If you right-click on a feature or scenario in the test case and click `Record Missing Steps in Feature/Scenario` then the test will execute the steps it knows and then pauses on the steps it doesn't know to record any button clicks and do any verification steps as according to the squish recording tools - see the tutorial on https://www.froglogic.com/squish/features/recording-and-playback/. After recording, this will insert the step function into a file in the steps section of the test suite resources - often this is in a file that doesn't make sense so please move it to somewhere it does make sense. 
 
-Although the recording is useful, it often produces brittle step functions, please make use of the utilities in the global scripts area to improve the robustness of the test and see https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/System-Testing-with-Squish#writing-tests for some hints, tips and gotchas.
+Although the recording is useful, it often produces brittle step functions, please make use of the utilities in the global scripts area to improve the robustness of the test and see [here](System-Testing-with-Squish) for some hints, tips and gotchas.
 
 ## Running the tests
 

doc/client/testing/System-Testing-with-Squish.md

@@ -192,7 +192,7 @@ Solution is to Rename `C:\Squish\python\msvcr90.dll` to `msvcr90_off.dll`, which
 
 ### Squish fails to begin run
 
-Attempt to change your tcb file to a regular neutron tcb file and begin a run. You should see it beginning and then return to set up with the log message: `invalid tcb start - must be 0 not 5.00000 ns`. See the [DAE troubleshooting](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/DAE-Trouble-Shooting) "invalid tcb start" section.
+Attempt to change your tcb file to a regular neutron tcb file and begin a run. You should see it beginning and then return to set up with the log message: `invalid tcb start - must be 0 not 5.00000 ns`. See the [DAE troubleshooting](/specific_iocs/dae/DAE-Trouble-Shooting) "invalid tcb start" section.
 
 ### Squish Fails to Start the Application
 

doc/client/troubleshooting/Java-Resource-Usage-Tools.md

@@ -26,7 +26,7 @@ Then edit your run configuration and include `-agentlib:hprof=heap=dump,format=b
 
 ## See also
 
-https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Debugging-memory-leaks-in-the-IBEX-GUI
+[Debugging memory leaks in the GUI](Debugging-memory-leaks-in-the-IBEX-GUI).
 
 ## JStack