diff --git a/docs/jargon.md b/docs/jargon.md
index 944ba6f..ac43646 100644
--- a/docs/jargon.md
+++ b/docs/jargon.md
@@ -32,9 +32,9 @@ Here are some definitions for common terms used in this documentation:
 
 **Library**: Allows distribution of C code about the filesystem. [Learn more about libraries](https://2066.medium.com/what-is-a-c-library-d5501c4a56fc)
 
-**Module**: Script that modifies your environment to include a package. See [environment modules](module-intro).
+**Module**: Script that modifies your environment to include a package. See [environment modules](software/module-intro.md).
 
-**Environment**: Set of environment variables. Defines the state of your current login **shell**. See [environment modules](module-intro).
+**Environment**: Set of environment variables. Defines the state of your current login **shell**. See [environment modules](software/module-intro.md).
 
 **Conda environment**: Set of installed packages. Activating a conda environment modifies your **shell** environment to include these packages. See [conda](software/conda.md).
 
diff --git a/docs/slurm/sbatch.md b/docs/slurm/sbatch.md
index d8b8972..5423087 100644
--- a/docs/slurm/sbatch.md
+++ b/docs/slurm/sbatch.md
@@ -26,4 +26,4 @@ This script should query the available GPUs, and print only one device to the sp
 
 If you need to run the same type of job over many inputs, different parameters, or even just some number of iterations, you should look into using [Job Arrays](arrays.md) to simplify your workflow.
 
-{% include-markdown "slurm-mail.md" %}
+{% include-markdown "slurm/slurm-mail.md" %}
diff --git a/docs/slurm/srun.md b/docs/slurm/srun.md
index e859761..0d14f03 100644
--- a/docs/slurm/srun.md
+++ b/docs/slurm/srun.md
@@ -28,4 +28,4 @@ srun -c 6 -p cpu --pty --x11 xclock
 !!! note
     You cannot run an interactive/gui job using the `sbatch` command, you must use `srun`.
 
-{% include-markdown "slurm-mail.md" %}
+{% include-markdown "slurm/slurm-mail.md" %}
diff --git a/docs/transition.md b/docs/transition.md
index 60ea694..8cf514e 100644
--- a/docs/transition.md
+++ b/docs/transition.md
@@ -87,14 +87,14 @@ Open OnDemand portal.
 ### Data Transfer
 
 For information about moving data to Unity, see our 
-[file transfer documentation](/managing-files/intro.html). 
+[file transfer documentation](managing-files/intro.md). 
 Please give yourself ample time to move your data ahead of the
 May 1, 2023 read-only freeze.
 
 ### Job Scheduler
 
 While the Shared Cluster uses LSF to allocate resources, Unity uses the
-[Slurm scheduler](/slurm/index.html). See
+[Slurm scheduler](slurm/index.md). See
 [this quick reference page](https://scicomp.ethz.ch/wiki/LSF_to_Slurm_quick_reference)
 for a comparison between LSF and Slurm options.
 
diff --git a/docs/updates/index.md b/docs/updates/index.md
index ddc42b1..c774296 100644
--- a/docs/updates/index.md
+++ b/docs/updates/index.md
@@ -1 +1 @@
-{% include-markdown "hierarchy-change.md" %}
+{% include-markdown "updates/hierarchy-change.md" %}