fixed broken links

Author: RobJY

docs/hpc/06_tools_and_software/01_software_on_greene.md

@@ -32,9 +32,9 @@ Below is a list of modules and their associated functions:
 
 
 ## Package Management for R, Python, & Julia, and Conda in general
--   [Conda environments (Python, R)](../06_tools_and_software/04_conda_environments.md)
--   [Using virtual environments for Python](../06_tools_and_software/02_python_packages_with_virtual_environments.md)
--   [Managing R packages with renv](../06_tools_and_software/03_r_packages_with_renv.md)
+-   [Conda environments (Python, R)](../06_tools_and_software/04_conda_environments.mdx)
+-   [Using virtual environments for Python](../06_tools_and_software/02_python_packages_with_virtual_environments.mdx)
+-   [Managing R packages with renv](../06_tools_and_software/03_r_packages_with_renv.mdx)
 
 ## Examples of software usage on Greene 
 Examples can be found under `/scratch/work/public/examples/` and include the following

docs/hpc/06_tools_and_software/05_sqlite_handling_large_structured_data.md

@@ -79,7 +79,7 @@ conda will install pre-compiled packages. Which is good (faster) and bad (not fu
 :::
 
 :::tip
-Alternative: install packages to a local directory or use renv as described in [R Packages with renv](./03_r_packages_with_renv.md)
+Alternative: install packages to a local directory or use renv as described in [R Packages with renv](./03_r_packages_with_renv.mdx)
 ```sh
 mkdir /scratch/$USER/projects/myTempProject
 cd  /scratch/$USER/projects/myTempProject