Making updates we discussed

[handwerkerd]

I'm making the updates we discussed in ME-ICA#959 (comment)

Changes proposed in this pull request (check marks are done):

• Move all info from log_extra_report to _comments in minimal.json and removed that field from that file
• Changed the ID for the tree from minimal_decision_tree_test1 to minimal_decision_tree and updated a test which checked for the ID (should have done that earlier)
• Added a placeholder reference to references.bib
• Add a real reference to references.bib when I create the project with a DOI on figshare
• Merge Lint codebase with additional style restrictions ME-ICA/tedana#970 into this tree
• Move all info from log_extra_report to _comments in kundu.json and removed that field from that file
• Depending how I feel, address Remove log_extra_report from decision tree configs ME-ICA/tedana#982 in this PR

@tsalo, it's your choice if you want to periodically merge my changes into your main PR or to wait until it's closer to done.