Render on a separate directory

[llrs-roche]

This works around the issue of rendering the file on the package installation directory. I think this could be the issue seen on the CI.

Note that there are two options&environmental variables to control where to copy the files and where to render the template. I hope this makes it easier on the CI than just a temporary directory for each package (my initial idea).

[Gotfrid]

Hi, I installed this in a devcontainer via pak::pak('pharmar/riskreports@fix_workarounds') and now report generation fails altogether with the following error:

ERROR: NotFound: No such file or directory (os error 2): readfile '../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js'
Path: ../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js

Stack trace:
Path: ../../workspaces/pharmapkgs/_pkg_template_files/libs/quarto-html/quarto.js
    at readTextFileSync (ext:deno_fs/30_fs.js:864:10)
    at Object.Deno.readTextFileSync (file:///opt/quarto/bin/quarto.js:5225:25)
    at bundleModules (file:///opt/quarto/bin/quarto.js:78339:56)
    at pandocIngestSelfContainedContent (file:///opt/quarto/bin/quarto.js:78350:11)
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async file:///opt/quarto/bin/quarto.js:78511:21
    at async withTimingAsync (file:///opt/quarto/bin/quarto.js:16980:25)
    at async Object.complete (file:///opt/quarto/bin/quarto.js:78506:13)
    at async Object.onPostProcess (file:///opt/quarto/bin/quarto.js:85977:36)
    at async renderFileInternal (file:///opt/quarto/bin/quarto.js:85961:5)
Warning message:
In quarto::quarto_render(template, output_format = "all", execute_params = params,  :
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed

I think it would be beneficial if you could write tests that run on a github runner to check if the issue is resolved. Without some kind of CI it is impossible to distinguish general problem fix from your specific environment changes (specific version of quarto, certain env variables, etc). Alternatively, please consider using a devcontainer for reproducible development.