New features to add to labnotes

[gaow]

• Inline get_output
• include block, include as is
• $xx block, decoration for specific format that will be ignored in others. This is an extension to the #{$ syntax. For example useful for quote in markdown
• Add RMarkdown style slides to publish slides in HTML.
• A utilities folder in the repo of SoS files for specific tasks, e.g. publish via bookdown
• Use bib format directly not json, see here
• --run: convert to SoS script, run SoS and then run notes
• Code blocks should allow for SoS options
• markedown support as input? That will help greatly but ... only to collaborations I guess. Mean while I can exploit git wiki for that!!
• In non-pdf context all figures in PDF are converted to png (need to do this after refactoring. now it is impossible). Same as the Run command it should be done in SoS so that cache is kept.
• Markdown footnote; make sure it is also possible to formally cite.
• Figure labels and refs only supported for markdown I guess ... Figure out the outcome of knitr for figure label and use that raw code {$xx inline. Labels can wait until after refactoring.
• Table from file. And perhaps via knitr and DT packages? Not sure if it worth the effort. Will see how it deals with regular table. Again the labeling part for table will copy from the output of md file. and also dig out the html widget interface (https://bookdown.org/yihui/bookdown/html-widgets.html). Make a shortcut for that to use with {$xx.
• Or, I should just figure out how knitr works outside R studio and provide a block called knitr to fully support it! This is mostly for tables and shiny app I believe, in which case PDF is no good anyways. Then will not have to convert that code back to labnotes for use with other formats. Will allow for the framework and see how it goes. Another option would be to faithfully pass those to the markdown file then use SoS to compile to all formats. That means document thus written cannot be used in regular labnotes PDF files.
• Also by default chop very long tables from PDF unless otherwise specified.
• Add base url option to all commands.
• Save all configureation files / templates in another format and build that to __ini__.py at compilation. Make configuration files more general, e.g., multiple files in same given folder.
• Change references to auto-numbering in ref, and footnote, applies for pdf, html and md.