Coding style fixes from clj-kondo's linter with default :off

[niyarin]

This issue is a answer to comment(#269 (comment))

• Lists options that clj-kondo defaults to :off that should be introduced.
• After listing, fix the corresponding code and add the clj-lint-action settings.

Linters that should be introduced

:single-key-in

• This option warns about get-in and update-in where the number of elements in keys is 1.
• Cljam reported 1 warning.

./src/cljam/io/fasta/reader.clj:74:39: warning: update-in with single key

:aliased-namespace-symbol

• This option warns about code that doesn't use namespace aliases.
• cljam reported 2 warnings.

./src/cljam/tools/cli.clj:332:32: warning: An alias is defined for clojure.java.io: cio
./src/cljam/tools/cli.clj:333:32: warning: An alias is defined for clojure.java.io: cio

Linters that may be introduced

:reduce-without-init
:redundant-fn-wrapper

Linters that may be introduced (without Kibit)

:minus-one :plus-one :equals-true