<p>Would you try</p>
<pre><code>codesign --verify --deep --strict --verbose=2 /Applications/Geany.app
</code></pre>
<p>if it gives some strange results? It should simulate the signature verification process that happens during execution. I get</p>
<pre><code>--prepared:/Applications/Geany.app/Contents/MacOS/geany-bin
--validated:/Applications/Geany.app/Contents/MacOS/geany-bin
/Applications/Geany.app: valid on disk
/Applications/Geany.app: satisfies its Designated Requirement
</code></pre>
<p>on my computer.</p>

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