Move libraries and applications from the tools directory to src

[underwoo]

Description
This moves the libraries and applications out of the tools directory, and puts
them in the src directory.

How Has This Been Tested?
Standard configure, make, make check, make distcheck on Mac OS (Arm and Intel), and several Linux OS systems.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included
• make distcheck passes

[underwoo]

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