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Establishes a pattern of "Getting Started" for introduction, and "Manual" for more involved usage.

I avoid populating docs/usage.rst here, since I suspect that #332, #292, and #329 might be really useful for external contributors. (We can automatically document config.yaml properties through Pydantic, and avoid downstream users for having to explicitly specify using the SPRAS snakefile)

@tristan-f-r tristan-f-r added the documentation Improvements or additions to documentation label Jul 21, 2025
@agitter agitter merged commit 292fae9 into Reed-CompBio:main Jul 23, 2025
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@tristan-f-r tristan-f-r deleted the docs-touch branch July 23, 2025 15:40
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