diff --git a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCachesManager.kt b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCachesManager.kt
index 83c8bb1f881..27dd6adbbcf 100644
--- a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCachesManager.kt
+++ b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCachesManager.kt
@@ -42,7 +42,7 @@ abstract class IncrementalCachesManager<PlatformCache : AbstractIncrementalCache
     private val inputSnapshotsCacheDir = File(cachesRootDir, "inputs").apply { mkdirs() }
     private val lookupCacheDir = File(cachesRootDir, "lookups").apply { mkdirs() }
 
-    val inputsCache: InputsCache = InputsCache(inputSnapshotsCacheDir, reporter).apply { registerCache() }
+    val inputsCache: InputsCache = InputsCache(inputSnapshotsCacheDir, reporter, pathConverter).apply { registerCache() }
     val lookupCache: LookupStorage = LookupStorage(lookupCacheDir, pathConverter).apply { registerCache() }
     abstract val platformCache: PlatformCache
 
diff --git a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/InputsCache.kt b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/InputsCache.kt
index fc4bb78c93c..e97cbd85af7 100644
--- a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/InputsCache.kt
+++ b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/InputsCache.kt
@@ -21,20 +21,22 @@ import org.jetbrains.kotlin.build.GeneratedFile
 import org.jetbrains.kotlin.build.report.ICReporter
 import org.jetbrains.kotlin.incremental.snapshots.FileSnapshotMap
 import org.jetbrains.kotlin.incremental.storage.BasicMapsOwner
+import org.jetbrains.kotlin.incremental.storage.FileToPathConverter
 import org.jetbrains.kotlin.incremental.storage.SourceToOutputFilesMap
 import java.io.File
 
 class InputsCache(
     workingDir: File,
-    private val reporter: ICReporter
+    private val reporter: ICReporter,
+    pathConverter: FileToPathConverter
 ) : BasicMapsOwner(workingDir) {
     companion object {
         private const val SOURCE_SNAPSHOTS = "source-snapshot"
         private const val SOURCE_TO_OUTPUT_FILES = "source-to-output"
     }
 
-    internal val sourceSnapshotMap = registerMap(FileSnapshotMap(SOURCE_SNAPSHOTS.storageFile))
-    private val sourceToOutputMap = registerMap(SourceToOutputFilesMap(SOURCE_TO_OUTPUT_FILES.storageFile))
+    internal val sourceSnapshotMap = registerMap(FileSnapshotMap(SOURCE_SNAPSHOTS.storageFile, pathConverter))
+    private val sourceToOutputMap = registerMap(SourceToOutputFilesMap(SOURCE_TO_OUTPUT_FILES.storageFile, pathConverter))
 
     fun removeOutputForSourceFiles(sources: Iterable<File>) {
         for (sourceFile in sources) {
diff --git a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMap.kt b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMap.kt
index 1db484b6346..d1055887f14 100644
--- a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMap.kt
+++ b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMap.kt
@@ -18,11 +18,16 @@ package org.jetbrains.kotlin.incremental.snapshots
 
 import org.jetbrains.kotlin.incremental.ChangedFiles
 import org.jetbrains.kotlin.incremental.storage.BasicStringMap
+import org.jetbrains.kotlin.incremental.storage.FileToPathConverter
 import org.jetbrains.kotlin.incremental.storage.PathStringDescriptor
 import java.io.File
 import java.util.*
 
-class FileSnapshotMap(storageFile: File) : BasicStringMap<FileSnapshot>(storageFile, PathStringDescriptor, FileSnapshotExternalizer) {
+class FileSnapshotMap(
+    storageFile: File,
+    private val pathConverter: FileToPathConverter
+) : BasicStringMap<FileSnapshot>(storageFile, PathStringDescriptor, FileSnapshotExternalizer) {
+
     override fun dumpValue(value: FileSnapshot): String =
         value.toString()
 
@@ -32,16 +37,16 @@ class FileSnapshotMap(storageFile: File) : BasicStringMap<FileSnapshot>(storageF
         val newOrModified = ArrayList<File>()
         val removed = ArrayList<File>()
 
-        val newPaths = newFiles.mapTo(HashSet()) { it.canonicalPath }
+        val newPaths = newFiles.mapTo(HashSet(), transform = pathConverter::toPath)
         for (oldPath in storage.keys) {
             if (oldPath !in newPaths) {
                 storage.remove(oldPath)
-                removed.add(File(oldPath))
+                removed.add(pathConverter.toFile(oldPath))
             }
         }
 
         for (path in newPaths) {
-            val file = File(path)
+            val file = pathConverter.toFile(path)
             val oldSnapshot = storage[path]
             val newSnapshot = snapshotProvider[file]
 
diff --git a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMap.kt b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMap.kt
index 28032db9d44..add1232cc16 100644
--- a/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMap.kt
+++ b/compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMap.kt
@@ -9,21 +9,22 @@ import org.jetbrains.kotlin.incremental.dumpCollection
 import java.io.File
 
 class SourceToOutputFilesMap(
-    storageFile: File
+    storageFile: File,
+    private val pathConverter: FileToPathConverter
 ) : BasicStringMap<Collection<String>>(storageFile, PathStringDescriptor, StringCollectionExternalizer) {
 
     @Synchronized
     operator fun set(sourceFile: File, outputFiles: Collection<File>) {
-        storage[sourceFile.absolutePath] = outputFiles.map { it.absolutePath }
+        storage[pathConverter.toPath(sourceFile)] = outputFiles.map(pathConverter::toPath)
     }
 
     operator fun get(sourceFile: File): Collection<File> =
-        storage[sourceFile.absolutePath].orEmpty().map(::File)
+        storage[pathConverter.toPath(sourceFile)].orEmpty().map(pathConverter::toFile)
 
     override fun dumpValue(value: Collection<String>) =
         value.dumpCollection()
 
     @Synchronized
     fun remove(file: File): Collection<File> =
-        get(file).also { storage.remove(file.absolutePath) }
+        get(file).also { storage.remove(pathConverter.toPath(file)) }
 }
\ No newline at end of file
diff --git a/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMapTest.kt b/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMapTest.kt
index 5bf918c5163..ec598b19b14 100644
--- a/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMapTest.kt
+++ b/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/snapshots/FileSnapshotMapTest.kt
@@ -6,6 +6,8 @@
 package org.jetbrains.kotlin.incremental.snapshots
 
 import org.jetbrains.kotlin.TestWithWorkingDir
+import org.jetbrains.kotlin.incremental.storage.FileToPathConverter
+import org.jetbrains.kotlin.incremental.storage.IncrementalFileToPathConverter
 import org.junit.After
 import org.junit.Assert.assertArrayEquals
 import org.junit.Before
@@ -15,13 +17,15 @@ import kotlin.properties.Delegates
 
 class FileSnapshotMapTest : TestWithWorkingDir() {
     private var snapshotMap: FileSnapshotMap by Delegates.notNull()
+    private var pathConverter: FileToPathConverter by Delegates.notNull()
 
     @Before
     override fun setUp() {
         super.setUp()
         val caches = File(workingDir, "caches").apply { mkdirs() }
         val snapshotMapFile = File(caches, "snapshots.tab")
-        snapshotMap = FileSnapshotMap(snapshotMapFile)
+        pathConverter = IncrementalFileToPathConverter((workingDir.canonicalFile))
+        snapshotMap = FileSnapshotMap(snapshotMapFile, pathConverter)
     }
 
     @After
diff --git a/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMapTest.kt b/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMapTest.kt
new file mode 100644
index 00000000000..240f870951f
--- /dev/null
+++ b/compiler/incremental-compilation-impl/test/org/jetbrains/kotlin/incremental/storage/SourceToOutputFilesMapTest.kt
@@ -0,0 +1,131 @@
+/*
+ * Copyright 2010-2020 JetBrains s.r.o. and Kotlin Programming Language contributors.
+ * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
+ */
+
+package org.jetbrains.kotlin.incremental.storage
+
+import org.jetbrains.kotlin.TestWithWorkingDir
+import org.junit.After
+import org.junit.Assert.assertArrayEquals
+import org.junit.Before
+import org.junit.Test
+import java.io.File
+import kotlin.properties.Delegates
+
+class SourceToOutputFilesMapTest : TestWithWorkingDir() {
+    private var stofMap: SourceToOutputFilesMap by Delegates.notNull()
+    private var pathConverter: FileToPathConverter by Delegates.notNull()
+
+    @Before
+    override fun setUp() {
+        super.setUp()
+        val caches = File(workingDir, "caches").apply { mkdirs() }
+        val stofMapFile = File(caches, "stof.tab")
+        pathConverter = IncrementalFileToPathConverter((workingDir.canonicalFile))
+        stofMap = SourceToOutputFilesMap(stofMapFile, pathConverter)
+    }
+
+    @After
+    override fun tearDown() {
+        stofMap.flush(false)
+        stofMap.close()
+        super.tearDown()
+    }
+
+    @Test
+    fun testEmptyGetReturnsEmpty() {
+        assertTrue(stofMap.get(File("")).isEmpty())
+    }
+
+    @Test
+    fun testSetGetOneReturnsOne() {
+        stofMap.set(
+            File(""),
+            listOf(File("one").canonicalFile))
+        assertEquals(
+            listOf(File("one").canonicalFile),
+            stofMap.get(File("")))
+    }
+
+    @Test
+    fun testSetDupeReturnsUnique() {
+        stofMap.set(
+            File(""),
+            listOf(File("one").canonicalFile, File("one").canonicalFile, File("one").canonicalFile))
+
+        assertEquals(
+            listOf(File("one").canonicalFile),
+            stofMap.get(File("")))
+    }
+
+    @Test
+    fun testSetOverwriteReturnsNew() {
+        stofMap.set(
+            File(""),
+            listOf(File("old").canonicalFile, File("old").canonicalFile, File("old").canonicalFile))
+        stofMap.set(
+            File(""),
+            listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile))
+
+        assertArrayEquals(
+            listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile).toSortedPaths(),
+            stofMap.get(File("")).toSortedPaths())
+    }
+
+    @Test
+    fun testRelativeInReturnsAbsolute() {
+        stofMap.set(
+            File(""),
+            listOf(File("one"), File("two"), File("three")))
+
+        assertArrayEquals(
+            listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile).toSortedPaths(),
+            stofMap.get(File("")).toSortedPaths()
+        )
+    }
+
+    @Test
+    fun testSetRelativeGetAbsolute() {
+        stofMap.set(
+            File("blah"),
+            listOf(File("one"), File("two"), File("three")))
+
+        assertArrayEquals(
+            listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile).toSortedPaths(),
+            stofMap.get(File("blah").canonicalFile).toSortedPaths()
+        )
+    }
+
+    @Test
+    fun testSetRemove() {
+        stofMap.set(
+            File("blah"),
+            listOf(File("one"), File("two"), File("three")))
+
+        assertArrayEquals(
+            listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile).toSortedPaths(),
+            stofMap.remove(File("blah")).toSortedPaths()
+        )
+        assertTrue(stofMap.get(File("blah")).isEmpty())
+    }
+
+    @Test
+    fun testSetRemoveLoop() {
+        repeat(5) {
+            stofMap.set(
+                File("blah"),
+                listOf(File("one"), File("two"), File("three"))
+            )
+
+            assertArrayEquals(
+                listOf(File("one").canonicalFile, File("two").canonicalFile, File("three").canonicalFile).toSortedPaths(),
+                stofMap.remove(File("blah")).toSortedPaths()
+            )
+            assertTrue(stofMap.get(File("blah")).isEmpty())
+        }
+    }
+
+    private fun Iterable<File>.toSortedPaths(): Array<String> =
+        map { it.canonicalPath }.sorted().toTypedArray()
+}
\ No newline at end of file