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Geany consumes 100% CPU by itself, no other process is involved. It does not show any excessive activity in the Disk tab. Startup attempts are logged in the Console Diagnostic Reports tab for excessive CPU, but otherwise there is nothing related to Geany there.
I have reinstalled the previous version ("Sulamar", details per original post) and can confirm that startup is then more or less instantaneous.
The only file types I have open are .sql (Oracle PL/SQL scripts) and simple .txt
One difference I notice between your build and Sulamar is that folders in the Documents tab are arranged as a hierarchy in yours (a huge improvement!) and as a single level without a hierarchy in Sulamar.
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