JPS: Fix updating cache format version for rebuilt targets by removing i/o optimization

Problem: previously, format-version.txt file was deleted while cleaning
target output on rebuild. Since directory was deleted, cache
attributesDiff stored in memory was not updated. This causes that on
saveExpectedStateIfNeeded does nothing.

The right way to fix it is move cache version format diff into
AbstractIncrementalCache, and override `clean()` method. But this is
hard to do for lookup storage, since used compilers set (jvm/js) will
known only after context init. This can be done by moving `expected`
attributes out of manager, but this is huge change for small benefit.

So, the optimal way for now is to write version for each build, even if
it is not changed.

#KT-27044 Fixed

compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCompilerRunner.kt

@@ -30,7 +30,6 @@ import org.jetbrains.kotlin.incremental.components.ExpectActualTracker
 import org.jetbrains.kotlin.incremental.components.LookupTracker
 import org.jetbrains.kotlin.incremental.parsing.classesFqNames
 import org.jetbrains.kotlin.incremental.storage.version.CacheVersionManager
-import org.jetbrains.kotlin.incremental.storage.version.saveIfNeeded
 import org.jetbrains.kotlin.name.FqName
 import org.jetbrains.kotlin.progress.CompilationCanceledStatus
 import java.io.File
@@ -272,7 +271,7 @@ abstract class IncrementalCompilerRunner<
         processChangesAfterBuild(compilationMode, currentBuildInfo, dirtyData)
 
         if (exitCode == ExitCode.OK) {
-            cachesVersionManagers.forEach { it.saveIfNeeded() }
+            cachesVersionManagers.forEach { it.writeVersion() }
         }
 
         return exitCode