Note the breaking change caused by afterEvaluate usages (#1719)

Author: Goooler

docs/changes/README.md

@@ -52,6 +52,7 @@
 
 - Don't inject `TargetJvmVersion` attribute when automatic JVM targeting is disabled. ([#1666](https://github.com/GradleUp/shadow/pull/1666))
 - Do not write modified class files for no-op relocations. ([#1694](https://github.com/GradleUp/shadow/pull/1694))
+- **BREAKING CHANGE:** The introduction of some `afterEvaluate` usages may cause configuration issues in rare cases.
 
 ## [9.0.2](https://github.com/GradleUp/shadow/releases/tag/9.0.2) - 2025-08-15