fixup some more links

Author: tomeichlersmith

book.toml

@@ -26,40 +26,40 @@ assets_version = "3.0.3" # do not edit: managed by `mdbook-admonish install`
 "/Dark-Brem-Signal-Process.html" = "/dark-brem/intro.html"
 "/docs/Alternative-Photo-Nuclear-Models.html" = "/Alternative-Photo-Nuclear-Models.html"
 "/Configuring-the-Simulation.html" = "/simulation/configuring.html"
-"/Running-and-configuring-fire.html" = "/fire/intro.html"
-"/fire-config-tips.html" = "/fire/config-tips.html"
-"/Structure-of-Event-Processors.html" = "/fire/structure-of-event-processors.html"
-"/Building-ldmx-sw.html" = "/building/intro.html"
-"/Building-ldmx-sw-containerless.html" = "/building/containerless.html"
-"/Contributing-to-ldmx-sw.html" = "/developers/Contributing-to-ldmx-sw.html"
-"/Creating-a-new-Event-Bus-Object.html" = "/developers/Creating-a-new-Event-Bus-Object.html"
-"/Logging.html" = "/developers/Logging.html"
-"/Unit-Testing-in-ldmx-sw.html" = "/developers/Unit-Testing-in-ldmx-sw.html"
-"/building/clusters.html" = "/developers/building/clusters.html"
-"/building/containerless.html" = "/developers/building/containerless.html"
-"/building/intro.html" = "/developers/building/intro.html"
-"/building/updating.html" = "/developers/building/updating.html"
-"/compatibility.html" = "/developers/compatibility.html"
-"/custom-production-image.html" = "/developers/custom-production-image.html"
-"/faq.html" = "/developers/faq.html"
-"/performance.html" = "/developers/performance.html"
-"/prs.html" = "/developers/prs.html"
-"/transition-to-ldmx-sw-v4.html" = "/developers/transition-to-ldmx-sw-v4.html"
-"/analysis/intro.html" = "/users/analysis/intro.html"
-"/analysis/ldmx-sw.html" = "/users/analysis/ldmx-sw.html"
-"/analysis/python.html" = "/users/analysis/python.html"
-"/config/config-basics.html" = "/users/config/config-basics.html"
-"/config/config-tips.html" = "/users/config/config-tips.html"
-"/config/drop-keep.html" = "/users/config/drop-keep.html"
-"/config/event-skimming.html" = "/users/config/event-skimming.html"
-"/config/intro.html" = "/users/config/intro.html"
-"/config/structure-of-event-processors.html" = "/users/config/structure-of-event-processors.html"
-"/dark-brem/how-to.html" = "/users/dark-brem/how-to.html"
-"/dark-brem/intro.html" = "/users/dark-brem/intro.html"
-"/dark-brem/legacy.html" = "/users/dark-brem/legacy.html"
-"/Alternative-Photo-Nuclear-Models.html" = "/users/sim/Alternative-Photo-Nuclear-Models.html"
-"/simulation/configuring.html" = "/users/sim/configuring.html"
-"/Generating-Simulation-Samples.html" = "/users/sim/generating.html"
-"/simulation/resim.html" = "/users/sim/resim.html"
-"/which-sim-particles.html" = "/users/sim/which-sim-particles.html"
-"/docker/index.html" = "/dev-build-context/index.html"
+"/Running-and-configuring-fire.html" = "/using/config/intro.html"
+"/fire-config-tips.html" = "/using/config/config-tips.html"
+"/Structure-of-Event-Processors.html" = "/using/config/structure-of-event-processors.html"
+"/Building-ldmx-sw.html" = "/developing/building/intro.html"
+"/Building-ldmx-sw-containerless.html" = "/developing/building/containerless.html"
+"/Contributing-to-ldmx-sw.html" = "/developing/Contributing-to-ldmx-sw.html"
+"/Creating-a-new-Event-Bus-Object.html" = "/developing/Creating-a-new-Event-Bus-Object.html"
+"/Logging.html" = "/developing/Logging.html"
+"/Unit-Testing-in-ldmx-sw.html" = "/developing/Unit-Testing-in-ldmx-sw.html"
+"/building/clusters.html" = "/developing/building/clusters.html"
+"/building/containerless.html" = "/developing/building/containerless.html"
+"/building/intro.html" = "/developing/building/intro.html"
+"/building/updating.html" = "/developing/building/updating.html"
+"/compatibility.html" = "/developing/compatibility.html"
+"/custom-production-image.html" = "/developing/custom-production-image.html"
+"/faq.html" = "/developing/faq.html"
+"/performance.html" = "/developing/performance.html"
+"/prs.html" = "/developing/prs.html"
+"/transition-to-ldmx-sw-v4.html" = "/developing/transition-to-ldmx-sw-v4.html"
+"/analysis/intro.html" = "/using/analysis/intro.html"
+"/analysis/ldmx-sw.html" = "/using/analysis/ldmx-sw.html"
+"/analysis/python.html" = "/using/analysis/python.html"
+"/config/config-basics.html" = "/using/config/config-basics.html"
+"/config/config-tips.html" = "/using/config/config-tips.html"
+"/config/drop-keep.html" = "/using/config/drop-keep.html"
+"/config/event-skimming.html" = "/using/config/event-skimming.html"
+"/config/intro.html" = "/using/config/intro.html"
+"/config/structure-of-event-processors.html" = "/using/config/structure-of-event-processors.html"
+"/dark-brem/how-to.html" = "/using/dark-brem/how-to.html"
+"/dark-brem/intro.html" = "/using/dark-brem/intro.html"
+"/dark-brem/legacy.html" = "/using/dark-brem/legacy.html"
+"/Alternative-Photo-Nuclear-Models.html" = "/using/sim/Alternative-Photo-Nuclear-Models.html"
+"/simulation/configuring.html" = "/using/sim/configuring.html"
+"/Generating-Simulation-Samples.html" = "/using/sim/generating.html"
+"/simulation/resim.html" = "/using/sim/resim.html"
+"/which-sim-particles.html" = "/using/sim/which-sim-particles.html"
+"/docker/index.html" = "/cpp_refman.html"

src/cpp_refman.html

@@ -10,9 +10,9 @@
       of putting other software manuals in their own GitHub pages and then linking them here
       like this.
     -->
-    <meta http-equiv="refresh" content="0; url='ldmx-sw/index.html'" />
+    <meta http-equiv="refresh" content="0; url='https://ldmx-software.github.io/ldmx-sw/index.html'" />
   </head>
   <body>
-    <a href="ldmx-sw/index.html" target="_blank">Click here to go to C++ Manual</a>
+    <a href="https://ldmx-software.github.io/ldmx-sw/index.html" target="_blank">Click here to go to C++ Manual</a>
   </body>
 </html>

src/developing/building/intro.md

@@ -4,7 +4,7 @@ There are many intricasies that come with building such a large software project
 This chapter is focused on providing guides on how to accomplish this build
 and more detailes related to it.
 
-This chapter assumes you already finished with everything under "[Getting started](../developing/getting-started.md)"
+This chapter assumes you already finished with everything under "[Getting started](../getting-started.md)"
 
 ## Clone the Software Repository
 In a terminal, go to the directory where you will keep all of your LDMX software and run the following command.

src/developing/custom-production-image.md

@@ -25,7 +25,7 @@ This included the ability for users of ldmx-sw to manually launch the workflow t
 #### Steps
 2. Add `omarmoreno` as a [collaborator](https://docs.docker.com/docker-hub/repos/#collaborators-and-their-role) on the new repository you created 
    (This is the username that will be pushing any generated production images to DockerHub).
-3. Go to the [Build Production Image]([200~https://github.com/LDMX-Software/ldmx-sw/actions/workflows/build_production_image.yml) workflow on the "Actions" page.
+3. Go to the [Build Production Image](https://github.com/LDMX-Software/ldmx-sw/actions/workflows/build_production_image.yml) workflow on the "Actions" page.
 4. Select "Run Workflow" and input your values for the three parameters. Leave the drop down menu to the value `trunk` - that is the branch on which the workflow is run.
    - `repo`: **required** DockerHub repository that you want the image to be pushed to (same as repo you created earlier - e.g. `tomeichlersmith/eat`)
    - `branch`: (optional) name of branch you want to be compiled into the production image (e.g. `iss420-my-cool-devs`, default is `trunk`)
@@ -90,5 +90,5 @@ A lot of different submission scripts have been written in `bash` and `python`,
 3. Submit the job script using the submission program (e.g. `bsub` or `condor`) however many times
 
 Some examples of submission scripts:
-- [ldmx-workflow/batch](https://github.com/LDMX-Software/ldmx-workflow/tree/master/batch)
-- [ldmx-sw-scripts/batch](https://github.com/LDMX-Software/ldmx-sw-scripts/tree/master/batch)
+- [ldmx-workflow/batch](https://github.com/LDMX-Software/ldmx-workflow)
+- [ldmx-sw-scripts/batch](https://github.com/LDMX-Software/ldmx-sw-scripts)

src/using/sim/which-sim-particles.md

@@ -43,7 +43,7 @@ as it interacts with the material. Most of these particles created during
 a shower are not "interesting" for our purposes, so it is helpful to just
 skip saving them. We do have the ability to store all of the particles in
 an event if you desire, you can follow 
-[the same instructions](simulation/resim.md#storing-all-simulated-particles)
+[the same instructions](resim.md#storing-all-simulated-particles)
 provided for storing all simulated particles during re-simulation.
 
 ## Implementation