Update index.md

Collegeville · May 24, 2022 · a580ab3 · a580ab3
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 # Organization
 JuliaPetra is organized into a series of layers.
-* The [Communications Layer](@ref) contains an interface for Single Program Multiple Data parallel systems
-* The [Problem Distribution Layer](@ref) manages how the problem is distributed across the processes
-* The [Linear Algebra Layer](@ref) provides the interfaces and implementations for linear algebra objects
+* The [Communications Layer](CommunicationLayer.md) contains an interface for Single Program Multiple Data parallel systems
+* The [Problem Distribution Layer](ProblemDistributionLayer.md) manages how the problem is distributed across the processes
+* The [Linear Algebra Layer](LinearAlgebraLayer.md) provides the interfaces and implementations for linear algebra objects