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docs: update links for 2.0 site
docs: update wiki to be developer-focused - replace many pages with links to new equivalent pages on the main site - remove unused support files
fix: fix documentation of command line args for Running PharmCAT
docs: add documentation about outside call format
docs: correct the command-line parameters for the Reporter module
docs: standardize Java links
docs: update Java requirement
docs: update Java requirement documentation
docs: don't use blockquote
docs: add warning emoji :sparkle:
docs: tweak docs to remind people to read VCF requirements
docs: update instructions for how to run PharmCAT components
docs: remove CLI flag for PharmCAT that's been removed from code
docs: update CLI options for PharmCAT jar
Improve "Running" docs based on user feedback
Change from "Astrolabe" to "OutsideCall" - refactor all the Astrolabe-specific references to "Outside Call" instead - we want to enable calls from any outside source that can supply their result in TSV-formatted files - Astrolabe is still used as a default example and we other calls to follow their format
Fix mentions of "pipeline" to "tool" - PharmCAT is not a pipeline, it's a tool that fits into a larger pipeline
Updated Running PharmCAT (markdown)
Update information about building PharmCAT * does not work with JDK9 ... yet
Update guideline links.
Add note about JDK
Tweak text.
Improve flow.
Update docs. Try to standardize arguments.
Add option for keeping matcher output.
Add docs for running PharmCAT