Change how to pass STDIN input via --file, rename other args

[SteveL-MSFT]

PR Summary

• Remove automatic reading of STDIN as it can block in environments that redirect STDIN but never send input like ADO Pipelines
• Use convention --file - to indicate to read from STDIN, updated CLI help
• Rename --format to --output-format to use -f to only mean --file, shorthand is now -o
• Rename --document to --input to have it consistent for config and resource invocation
• Rename --trace-format shorthand to -t
• Lots of test changes due to the parameters change

PR Context

Fix #588