LSP does not recognize subprojects

[skinmaker1345]

Issue

Kotlin LSP does not recognize / properly index subprojects, since v0.253.10629.

v0.252

v0.253

We could see the message saying Package directive does not match the file location(PackageDirectoryMismatch) when hovering the mouse over the directive of the package(on top of the file).
Also, several errors occur, saying:

invalidated at: no info
  Code: -32803 
2025-08-07 03:20:56,559 [  40516] SEVERE - #c.j.l.i.LspClient - 
Element: class org.jetbrains.kotlin.analysis.api.fir.symbols.KtPackage #JAVA  because: parent is null
invalidated at: no info
com.intellij.diagnostic.PluginException: Element: class org.jetbrains.kotlin.analysis.api.fir.symbols.KtPackage #JAVA  because: parent is null
invalidated at: no info
	at com.intellij.diagnostic.PluginProblemReporterImpl.createPluginExceptionByClass(PluginProblemReporterImpl.java:23)
	at com.intellij.diagnostic.PluginException.createByClass(PluginException.java:100)
	at com.intellij.psi.util.PsiUtilCore.ensureValid(PsiUtilCore.java:508)
	at com.intellij.psi.impl.source.resolve.ResolveCache.ensureValidPsi(ResolveCache.java:255)
	at com.intellij.psi.impl.source.resolve.ResolveCache.ensureValidResults(ResolveCache.java:248)
	at com.intellij.psi.impl.source.resolve.ResolveCache.resolve(ResolveCache.java:226)
	at com.intellij.psi.impl.source.resolve.ResolveCache.resolveWithCaching(ResolveCache.java:166)
	at com.intellij.psi.impl.source.resolve.ResolveCache.resolveWithCaching(ResolveCache.java:148)
	at org.jetbrains.kotlin.idea.references.AbstractKtReference.multiResolve(KtReference.kt:34)
	at com.intellij.psi.PsiPolyVariantReferenceBase.resolve(PsiPolyVariantReferenceBase.java:32)
	at com.jetbrains.ls.api.features.impl.common.kotlin.definitions.LSKotlinPackageDefinitionProvider$provideDefinitions$1$1.invokeSuspend$lambda$3(LSKotlinPackageDefinitionProvider.kt:41)
	at com.intellij.openapi.application.ActionsKt.runReadAction$lambda$3(actions.kt:25)
	at com.jetbrains.analyzer.bootstrap.AnalyzerApplication$runReadAction$2.invoke(AnalyzerApplication.kt:37)
<--- omitted --->

[strangepleasures]

Thanks for reporting!