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Troubleshooting
Official releases are signed and notarized by Apple, so they open without this warning. If you see it, you most likely have a build from somewhere other than the releases page, or an older unsigned version. Download the current build from the latest release. If you still need to open an unsigned copy, right-click the app, choose Open, and confirm once.
For a Mermaid diagram, check that the code fence is tagged mermaid and that the diagram syntax is valid. For math, make sure inline expressions sit between single dollar signs and blocks between double dollar signs. A stray or missing dollar sign is the usual cause.
If a document has never been saved, ⌘S asks where to put it. After that, saving writes back to the same file. A dot beside the file name means there are unsaved changes waiting.
That is live reload at work: when the file changes on disk, Markappoly refreshes it. It only does this when you have no unsaved edits, so it will not clobber your work. To keep a file still, avoid editing it elsewhere while it is open.
Set Markappoly as the default app for Markdown files. On macOS, right-click a .md file, choose Get Info, set "Open with" to Markappoly, and click "Change All". On Windows, right-click the file, choose "Open with", then "Choose another app", and pick Markappoly with the "Always" option.
If you hit a bug or have a request, open an issue at appoly/markappoly/issues.