fix: Options not written before use

[mhovd]

Changes:

• PMoptions.R — getPMoptions() now prefers the user file but falls back to the packaged defaults when it's missing (or the path is NA), so it never returns -1 when sane defaults ship with the package.
• PMoptions.R — setPMoptions() now writes options first and only builds/launches the Shiny app when launch.app = TRUE, so the package-load path no longer depends on constructing the app.
• PMoptions.R — dir.create() is now recursive = TRUE. PM_report.R — the HTML fallback now normalizes any unrecognized template ("app", -1, NULL) to a valid default instead of erroring in switch().

Resolves #304

[Copilot]

Pull request overview

This PR addresses first-install/report-generation failures caused by missing user option files by making option loading more robust and ensuring defaults are persisted before any interactive UI is constructed.

Changes:

• Update getPMoptions() to prefer the user options file but fall back to packaged defaults when the user file is missing/invalid.
• Update setPMoptions() to write/sync options before optionally building and launching the Shiny options app; also create the options directory recursively.
• Harden PM_report() HTML fallback behavior by normalizing invalid/unrecognized templates to a valid default before switch().

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
R/PMoptions.R	Ensures defaults are discoverable on fresh install and decouples options persistence from launching the Shiny UI.
R/PM_report.R	Prevents HTML fallback report generation from erroring on invalid/legacy option values for report_template.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.