Relationship between (old) linter and (new) diagnostics? - packages - Atom Discussion
The difference is that the linter packages use different external programs to analyze the code and the atom-ide packages use Language Server Protocol 87 implementations (which are just another, more standardized way of solving the same problem).
I imagine people will use one or the other depending on what they're familiar with and what they need out of code checking, but at the moment I don't know of any reason why LSP isn't an unqualified upgrade.
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