Updates to README and documentation

Small updates to README and documentation website.

README:

• Remove deprecated Jenkins status badge

• Add Zenodo DOI badge

• Tweak formatting

• Update citation section of README:

  • Remove static reference to current version's DOI that needs manual changing with new releases. (The Zenodo badge is also static, but it much more prominent)

  • Say that using a specific version’s DOI is preferred

Website docs

• Make the Manual link to each sections' main page (rather than the directory)

• Update release instructions to give specific instructions for merging master to next

• Add point in release instructions for updating DOIs and release info in README and CITATION.cff