thedesk/app/node_modules/app-builder-lib/templates/nsis

It is developer documentation. See user documentation.

http://www.mathiaswestin.net/2012/09/how-to-make-per-user-installation-with.html

https://msdn.microsoft.com/en-us/library/windows/desktop/dd378457(v=vs.85).aspx#FOLDERID_UserProgramFiles

https://github.com/Drizin/NsisMultiUser

NSIS vs Inno Setup — it is not easy to choose because both are far from ideal, e.g. inno also doesn't have built-in per-user installation implementation — http://stackoverflow.com/questions/34330668/inno-setup-custom-dialog-with-per-user-or-per-machine-installation.

http://stackoverflow.com/questions/2565215/checking-if-the-application-is-running-in-nsis-before-uninstalling

One-click installer: http://forums.winamp.com/showthread.php?t=300479

GUID

See docs.

We use UUID v5 to generate sha-1 name-based UUID.

http://stackoverflow.com/questions/3029994/convert-uri-to-guid
https://alexandrebrisebois.wordpress.com/2013/11/14/create-predictable-guids-for-your-windows-azure-table-storage-entities/
https://github.com/Squirrel/Squirrel.Windows/pull/658

Compression

NSIS LZMA compression is slower and worse compared to external 7za compression. Slower because 7za is multi-threaded, worse because LZMA codec implementation is outdated and BCJ2 filter is not enabled.
Difference for test app — 4 MB (before: 36.3 after: 32.8).

And compression time is also greatly reduced.

Since NSIS is awesome, no disadvantages in our approach — compression is disabled before File /oname=app.7z "${APP_ARCHIVE}" and enabled after (it is the reasons why SOLID compression is not used).
So, opposite to Squirrel.Windows, archive is not twice compressed.

So, in your custom NSIS scripts you should not use any compression instructions. Only SetCompress if you need to disable compression for already archived file.