Refactor the layout of the applications

[underwoo]

Placing the tools in the postprocessing and tools directories is a remnant of when we used CVS and does not reflect how we manage the repository now or how the tools are used in the FRE workflow. The repository should be reconfigured to place the applications in one directory and supporting libraries in a second—this will help with maintaining the repository and updating the building framework.

[mlee03]

Marking it as a milestone for 2025.01 since I think PR #338 is the last one in the series of PRs (#322, #331, and #337) for this issue.