Reimplement the CLI in TypeScript

[bmesuere]

The ruby cli client became hard to maintain. The script for publishing new versions breaks every release and there were some problems getting this to work on windows. In addition, the use of native code required a compilation step during installation which often caused issues. The goal is to develop a drop-in replacement.

• port the uniprot command
• set up testing and linting
• port peptfilter + benchmark
• port prot2pept + benchmark
• add fasta support
• implement all formatters
  • xml
  • csv
  • json
• implement the unipept commands
• add error log support
• catch error when piping to head -n1
• publish as CLI on npm

Breaking changes

• no more config file support

These are not really breaking changes since they are also broken in the current ruby tool.

• The taxa2tree command wasn't added because this uses the broken blocks website.
• The --meganize flag of the pept2prot command wasn't ported since this relied on fields no longer present in the database.

Copilot reviewed 122 out of 137 changed files in this pull request and generated no suggestions.

Files not reviewed (15)

• .devcontainer/devcontainer.json: Language not supported
• .document: Language not supported
• .nvmrc: Language not supported
• .rakeTasks: Language not supported
• .rubocop.yml: Language not supported
• .ruby-version: Language not supported
• .vscode/tasks.json: Language not supported
• Gemfile: Language not supported
• Rakefile: Language not supported
• VERSION: Language not supported
• lib/batch_iterator.rb: Evaluated as low risk
• lib/batch_order.rb: Evaluated as low risk
• lib/commands.rb: Evaluated as low risk
• lib/commands/peptfilter.rb: Evaluated as low risk
• .github/workflows/ci.yml: Evaluated as low risk