From 8c4f93042071115027b70cd76bc8053c3bf11ece Mon Sep 17 00:00:00 2001
From: guijacquemet <guillaume.jacquemet@abo.fi>
Date: Wed, 14 Oct 2026 11:20:29 +0000
Subject: [PATCH] README: say that the GUI test harness modifies the QuPath
 installation

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 0eb98de..9e8535f 100644
--- a/README.md
+++ b/README.md
@@ -138,6 +138,8 @@ Users get the jar from the Releases page (see Install). Developers: `QUPATH=/pat
     QUPATH=/path/to/QuPath JAVA_HOME=<JDK 25> ./build.sh        # QuPath 0.7 is built with Java 25
     QUPATH=/path/to/QuPath LC_HOME=<registry with NucleiSky and CellTracksColab> tests/run_gui_test.sh   # needs xvfb; 21 checks
 
+**The GUI test harness modifies the QuPath installation you point `QUPATH` at**: `tests/run_gui_test.sh` copies the jar into `$QUPATH/lib/app/` and edits `$QUPATH/lib/app/QuPath.cfg` (it adds the jar to `app.classpath`). Use a disposable copy of QuPath, not the one you work in.
+
 `BODY=gui_test_interactions_body.groovy tests/run_gui_test.sh` runs the interaction hints, messages and points against the example app of labconstrictor-tools (`labconstrictor_tools.examples.interactions`, registered in `LC_HOME`; 9 checks).
 
 `BODY=gui_test_playground_body.groovy tests/run_gui_test.sh` runs the tools of the LabConstrictor Playground app (check, device dropdown, big image, crash, no memory, 200 000 points; 8 checks; register the Playground in `LC_HOME` first).