Group files under top level directories (!91)

docs/source_docs/index.rst

@@ -55,12 +55,12 @@ To learn more about the implementation, follow the following reference sections:
 
    references/units
    references/size_distributions
-   ManagingGridHierarchy_Chapter
-   Fluids_Chapter
-   Particles_Chapter
-   EB_Chapter
+   references/ManagingGridHierarchy_Chapter
+   references/Fluids_Chapter
+   references/Particles_Chapter
+   references/EB_Chapter
    references/hpc
-   Debugging
+   references/Debugging
    works_cited
 
 .. toctree::
@@ -76,11 +76,11 @@ and performance:
    :maxdepth: 0
    :caption: Tests and Benchmarks:
 
-   RunningTestSuite
-   RegressionTesting
-   CITests
-   NightlyTests
-   qb/index
+   test_benchmarks/RunningTestSuite
+   test_benchmarks/RegressionTesting
+   test_benchmarks/CITests
+   test_benchmarks/NightlyTests
+   test_benchmarks/qualitative_bencharks/index
 
 Notice
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