diff --git a/advisor/src/main/kotlin/Advisor.kt b/advisor/src/main/kotlin/Advisor.kt
index d65541b104e42..c85aa0c5e6b6b 100644
--- a/advisor/src/main/kotlin/Advisor.kt
+++ b/advisor/src/main/kotlin/Advisor.kt
@@ -66,8 +66,16 @@ class Advisor(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
-        requireNotNull(ortResult.analyzer) {
-            "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        if (ortResult.analyzer == null) {
+            log.warn {
+                "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+            }
+
+            return ortResult
         }
 
         val providers = providerFactories.map { it.create(config) }
diff --git a/advisor/src/test/kotlin/advisors/VulnerableCodeTest.kt b/advisor/src/test/kotlin/advisors/VulnerableCodeTest.kt
index d6fd669fce2a0..393d005d69144 100644
--- a/advisor/src/test/kotlin/advisors/VulnerableCodeTest.kt
+++ b/advisor/src/test/kotlin/advisors/VulnerableCodeTest.kt
@@ -92,7 +92,8 @@ class VulnerableCodeTest : WordSpec({
             stubVulnerability("v3", "CVE-2019-CoV19", 77.0f)
 
             val vulnerableCode = createVulnerableCode(wiremock)
-            val packagesToAdvise = resultFile().readValue<OrtResult>().getPackages(false).map { it.pkg }
+            val ortResult = resultFile().readValue<OrtResult>()
+            val packagesToAdvise = ortResult?.getPackages(false)?.map { it.pkg }.orEmpty()
 
             val result = vulnerableCode.retrievePackageVulnerabilities(packagesToAdvise).mapKeys { it.key.id }
 
@@ -145,7 +146,8 @@ class VulnerableCodeTest : WordSpec({
             )
 
             val vulnerableCode = createVulnerableCode(wiremock)
-            val packagesToAdvise = resultFile().readValue<OrtResult>().getPackages(false).map { it.pkg }
+            val ortResult = resultFile().readValue<OrtResult>()
+            val packagesToAdvise = ortResult?.getPackages(false)?.map { it.pkg }.orEmpty()
 
             vulnerableCode.retrievePackageVulnerabilities(packagesToAdvise).mapKeys { it.key.id } shouldNotBeNull {
                 val strutsResults = getValue(idStruts)
@@ -235,7 +237,8 @@ private val vulnerabilityDetailsTemplate = File(TEST_FILES_ROOT).resolve(VULNERA
  */
 private fun expectErrorResult(wiremock: WireMockServer) {
     val vulnerableCode = createVulnerableCode(wiremock)
-    val packagesToAdvise = resultFile().readValue<OrtResult>().getPackages(false).map { it.pkg }
+    val ortResult = resultFile().readValue<OrtResult>()
+    val packagesToAdvise = ortResult?.getPackages(false)?.map { it.pkg }.orEmpty()
 
     val result = runBlocking {
         vulnerableCode.retrievePackageVulnerabilities(packagesToAdvise).mapKeys { it.key.id }
diff --git a/analyzer/src/main/kotlin/Analyzer.kt b/analyzer/src/main/kotlin/Analyzer.kt
index 675746fde7d2f..0655d2fd60ecd 100644
--- a/analyzer/src/main/kotlin/Analyzer.kt
+++ b/analyzer/src/main/kotlin/Analyzer.kt
@@ -60,7 +60,7 @@ class Analyzer(private val config: AnalyzerConfiguration) {
         val repositoryConfiguration = if (actualRepositoryConfigurationFile.isFile) {
             log.info { "Using configuration file '${actualRepositoryConfigurationFile.absolutePath}'." }
 
-            actualRepositoryConfigurationFile.readValue()
+            actualRepositoryConfigurationFile.readValue() ?: RepositoryConfiguration()
         } else {
             RepositoryConfiguration()
         }
diff --git a/analyzer/src/main/kotlin/curation/FilePackageCurationProvider.kt b/analyzer/src/main/kotlin/curation/FilePackageCurationProvider.kt
index 31413d541b8cc..4ab1a8e28b802 100644
--- a/analyzer/src/main/kotlin/curation/FilePackageCurationProvider.kt
+++ b/analyzer/src/main/kotlin/curation/FilePackageCurationProvider.kt
@@ -33,7 +33,7 @@ import org.ossreviewtoolkit.model.readValue
  */
 class FilePackageCurationProvider(curationFile: File) : PackageCurationProvider {
     internal val packageCurations: List<PackageCuration> by lazy {
-        curationFile.readValue<List<PackageCuration>>()
+        curationFile.readValue<List<PackageCuration>>().orEmpty()
     }
 
     override fun getCurationsFor(pkgId: Identifier) = packageCurations.filter { it.isApplicable(pkgId) }
diff --git a/analyzer/src/main/kotlin/managers/Npm.kt b/analyzer/src/main/kotlin/managers/Npm.kt
index 93869123d50de..df8a9f4fa267c 100644
--- a/analyzer/src/main/kotlin/managers/Npm.kt
+++ b/analyzer/src/main/kotlin/managers/Npm.kt
@@ -226,7 +226,7 @@ open class Npm(
 
             log.debug { "Found a 'package.json' file in '$packageDir'." }
 
-            val json = it.readValue<ObjectNode>()
+            val json = it.readValue<ObjectNode>() ?: return@forEach
             val rawName = json["name"].textValue()
             val (namespace, name) = splitNamespaceAndName(rawName)
             val version = json["version"].textValue()
diff --git a/analyzer/src/main/kotlin/managers/utils/NodeSupport.kt b/analyzer/src/main/kotlin/managers/utils/NodeSupport.kt
index 58303b52b2211..a9b1e628842b6 100644
--- a/analyzer/src/main/kotlin/managers/utils/NodeSupport.kt
+++ b/analyzer/src/main/kotlin/managers/utils/NodeSupport.kt
@@ -23,13 +23,12 @@ package org.ossreviewtoolkit.analyzer.managers.utils
 
 import com.fasterxml.jackson.core.JsonProcessingException
 import com.fasterxml.jackson.databind.node.ArrayNode
-import com.fasterxml.jackson.databind.node.ObjectNode
 
 import java.io.File
 import java.nio.file.FileSystems
 import java.nio.file.PathMatcher
 
-import org.ossreviewtoolkit.model.readValue
+import org.ossreviewtoolkit.model.readJsonFile
 import org.ossreviewtoolkit.utils.AuthenticatedProxy
 import org.ossreviewtoolkit.utils.ProtocolProxyMap
 import org.ossreviewtoolkit.utils.collectMessagesAsString
@@ -176,7 +175,7 @@ private fun getPackageJsonInfo(definitionFiles: Set<File>): Collection<PackageJs
 
 private fun isYarnWorkspaceRoot(definitionFile: File) =
     try {
-        definitionFile.readValue<ObjectNode>()["workspaces"] != null
+        readJsonFile(definitionFile).has("workspaces")
     } catch (e: JsonProcessingException) {
         e.showStackTrace()
 
@@ -211,7 +210,7 @@ private fun getYarnWorkspaceSubmodules(definitionFiles: Set<File>): Set<File> {
 
 private fun getWorkspaceMatchers(definitionFile: File): List<PathMatcher> {
     var workspaces = try {
-        definitionFile.readValue<ObjectNode>()["workspaces"]
+        readJsonFile(definitionFile).get("workspaces")
     } catch (e: JsonProcessingException) {
         e.showStackTrace()
 
diff --git a/cli/src/funTest/kotlin/ExamplesFunTest.kt b/cli/src/funTest/kotlin/ExamplesFunTest.kt
index 14cae6770116e..18de6e1410a35 100644
--- a/cli/src/funTest/kotlin/ExamplesFunTest.kt
+++ b/cli/src/funTest/kotlin/ExamplesFunTest.kt
@@ -93,8 +93,8 @@ class ExamplesFunTest : StringSpec() {
 
         "license-classifications.yml can be deserialized" {
             shouldNotThrow<IOException> {
-                val classifications =
-                    takeExampleFile("license-classifications.yml").readValue<LicenseClassifications>()
+                val classifications = takeExampleFile("license-classifications.yml").readValue()
+                    ?: LicenseClassifications()
 
                 classifications.categories.filter { it.description.isNotEmpty() } shouldNot beEmpty()
                 classifications.categoryNames shouldContain "public-domain"
@@ -130,19 +130,21 @@ class ExamplesFunTest : StringSpec() {
             val resultFile = File("src/funTest/assets/semver4j-analyzer-result.yml")
             val licenseFile = File("../examples/license-classifications.yml")
             val ortResult = resultFile.readValue<OrtResult>()
-            val evaluator = Evaluator(
-                ortResult = ortResult,
-                licenseInfoResolver = ortResult.createLicenseInfoResolver(),
-                licenseClassifications = licenseFile.readValue()
-            )
 
-            val script = takeExampleFile("rules.kts").readText()
+            ortResult shouldNotBeNull {
+                val evaluator = Evaluator(
+                    ortResult = this,
+                    licenseInfoResolver = createLicenseInfoResolver(),
+                    licenseClassifications = licenseFile.readValue() ?: LicenseClassifications()
+                )
 
-            val result = evaluator.run(script)
+                val script = takeExampleFile("rules.kts").readText()
+                val result = evaluator.run(script)
 
-            result.violations shouldHaveSize 2
-            val failedRules = result.violations.map { it.rule }
-            failedRules shouldContainExactlyInAnyOrder listOf("UNHANDLED_LICENSE", "COPYLEFT_LIMITED_IN_SOURCE")
+                result.violations shouldHaveSize 2
+                val failedRules = result.violations.map { it.rule }
+                failedRules shouldContainExactlyInAnyOrder listOf("UNHANDLED_LICENSE", "COPYLEFT_LIMITED_IN_SOURCE")
+            }
         }
 
         "asciidoctor-pdf-theme.yml is a valid asciidoctor-pdf theme" {
diff --git a/cli/src/main/kotlin/commands/DownloaderCommand.kt b/cli/src/main/kotlin/commands/DownloaderCommand.kt
index 0a7f5f9f9b66c..e9f483b7b8cf5 100644
--- a/cli/src/main/kotlin/commands/DownloaderCommand.kt
+++ b/cli/src/main/kotlin/commands/DownloaderCommand.kt
@@ -180,15 +180,25 @@ class DownloaderCommand : CliktCommand(name = "download", help = "Fetch source c
         when (input) {
             is FileType -> {
                 val ortFile = (input as FileType).file
-                val (analyzerResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>().analyzer?.result }
+                val (ortResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>() }
 
                 log.perf {
                     "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in " +
                             "${duration.inMilliseconds}ms."
                 }
 
-                requireNotNull(analyzerResult) {
-                    "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+                requireNotNull(ortResult) {
+                    "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+                }
+
+                val analyzerResult = ortResult.analyzer?.result
+
+                if (analyzerResult == null) {
+                    log.warn {
+                        "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+                    }
+
+                    throw ProgramResult(0)
                 }
 
                 val packages = mutableListOf<Package>().apply {
diff --git a/cli/src/main/kotlin/commands/EvaluatorCommand.kt b/cli/src/main/kotlin/commands/EvaluatorCommand.kt
index 04fc7c9132ad3..41c784522f9f2 100644
--- a/cli/src/main/kotlin/commands/EvaluatorCommand.kt
+++ b/cli/src/main/kotlin/commands/EvaluatorCommand.kt
@@ -45,9 +45,11 @@ import org.ossreviewtoolkit.GroupTypes.StringType
 import org.ossreviewtoolkit.evaluator.Evaluator
 import org.ossreviewtoolkit.model.FileFormat
 import org.ossreviewtoolkit.model.OrtResult
+import org.ossreviewtoolkit.model.PackageCuration
 import org.ossreviewtoolkit.model.Severity
 import org.ossreviewtoolkit.model.config.CopyrightGarbage
 import org.ossreviewtoolkit.model.config.LicenseFilenamePatterns
+import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.config.createFileArchiver
 import org.ossreviewtoolkit.model.config.orEmpty
 import org.ossreviewtoolkit.model.licenses.DefaultLicenseInfoProvider
@@ -239,12 +241,12 @@ class EvaluatorCommand : CliktCommand(name = "evaluate", help = "Evaluate ORT re
             }
         }
 
-        repositoryConfigurationFile?.let {
-            ortResultInput = ortResultInput?.replaceConfig(it.readValue())
+        repositoryConfigurationFile?.readValue<RepositoryConfiguration>()?.let {
+            ortResultInput = ortResultInput?.replaceConfig(it)
         }
 
-        packageCurationsFile?.let {
-            ortResultInput = ortResultInput?.replacePackageCurations(it.readValue())
+        packageCurationsFile?.readValue<List<PackageCuration>>()?.let {
+            ortResultInput = ortResultInput?.replacePackageCurations(it)
         }
 
         val finalOrtResult = requireNotNull(ortResultInput) {
diff --git a/cli/src/main/kotlin/commands/ReporterCommand.kt b/cli/src/main/kotlin/commands/ReporterCommand.kt
index 16ee758347596..6767e69b90169 100644
--- a/cli/src/main/kotlin/commands/ReporterCommand.kt
+++ b/cli/src/main/kotlin/commands/ReporterCommand.kt
@@ -45,6 +45,7 @@ import org.ossreviewtoolkit.GlobalOptions
 import org.ossreviewtoolkit.model.OrtResult
 import org.ossreviewtoolkit.model.config.CopyrightGarbage
 import org.ossreviewtoolkit.model.config.LicenseFilenamePatterns
+import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.config.Resolutions
 import org.ossreviewtoolkit.model.config.createFileArchiver
 import org.ossreviewtoolkit.model.config.orEmpty
@@ -200,14 +201,18 @@ class ReporterCommand : CliktCommand(
     private val globalOptionsForSubcommands by requireObject<GlobalOptions>()
 
     override fun run() {
-        var (ortResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>() }
+        var (originalOrtResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>() }
 
         log.perf {
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
-        repositoryConfigurationFile?.let {
-            ortResult = ortResult.replaceConfig(it.readValue())
+        repositoryConfigurationFile?.readValue<RepositoryConfiguration>()?.let {
+            originalOrtResult = originalOrtResult?.replaceConfig(it)
+        }
+
+        val ortResult = requireNotNull(originalOrtResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
         }
 
         val resolutionProvider = DefaultResolutionProvider()
diff --git a/cli/src/main/kotlin/commands/UploadCurationsCommand.kt b/cli/src/main/kotlin/commands/UploadCurationsCommand.kt
index 4e388a2a94e54..bfc4c31d29413 100644
--- a/cli/src/main/kotlin/commands/UploadCurationsCommand.kt
+++ b/cli/src/main/kotlin/commands/UploadCurationsCommand.kt
@@ -95,7 +95,7 @@ class UploadCurationsCommand : CliktCommand(
         }
 
     override fun run() {
-        val curations = inputFile.readValue<List<PackageCuration>>()
+        val curations = inputFile.readValue<List<PackageCuration>>().orEmpty()
         val curationsToCoordinates = curations.associateWith { it.id.toClearlyDefinedCoordinates().toString() }
         val definitions = service.call { getDefinitions(curationsToCoordinates.values) }
 
diff --git a/cli/src/main/kotlin/commands/UploadResultToPostgresCommand.kt b/cli/src/main/kotlin/commands/UploadResultToPostgresCommand.kt
index c733e0286b500..9b2043d0da7e8 100644
--- a/cli/src/main/kotlin/commands/UploadResultToPostgresCommand.kt
+++ b/cli/src/main/kotlin/commands/UploadResultToPostgresCommand.kt
@@ -93,6 +93,10 @@ class UploadResultToPostgresCommand : CliktCommand(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val postgresConfig = globalOptionsForSubcommands.config.scanner.storages?.values
             ?.filterIsInstance<PostgresStorageConfiguration>()?.singleOrNull()
 
diff --git a/cli/src/main/kotlin/commands/UploadResultToSw360Command.kt b/cli/src/main/kotlin/commands/UploadResultToSw360Command.kt
index dc7b7040420f8..d7f13f1cc6dac 100644
--- a/cli/src/main/kotlin/commands/UploadResultToSw360Command.kt
+++ b/cli/src/main/kotlin/commands/UploadResultToSw360Command.kt
@@ -82,6 +82,10 @@ class UploadResultToSw360Command : CliktCommand(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val sw360Config = globalOptionsForSubcommands.config.scanner.storages?.values
             ?.filterIsInstance<Sw360StorageConfiguration>()?.singleOrNull()
 
diff --git a/helper-cli/src/main/kotlin/commands/ExportLicenseFindingCurationsCommand.kt b/helper-cli/src/main/kotlin/commands/ExportLicenseFindingCurationsCommand.kt
index c14972334a342..277c80348c9ee 100644
--- a/helper-cli/src/main/kotlin/commands/ExportLicenseFindingCurationsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ExportLicenseFindingCurationsCommand.kt
@@ -71,16 +71,16 @@ internal class ExportLicenseFindingCurationsCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val localLicenseFindingCurations = ortFile
-            .readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        val localLicenseFindingCurations = ortResult
             .replaceConfig(repositoryConfigurationFile)
             .getRepositoryLicenseFindingCurations()
 
-        val globalLicenseFindingCurations = if (licenseFindingCurationsFile.isFile) {
-            licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>()
-        } else {
-            mapOf()
-        }
+        val globalLicenseFindingCurations = licenseFindingCurationsFile.takeIf { it.isFile }
+            ?.readValue<RepositoryLicenseFindingCurations>().orEmpty()
 
         globalLicenseFindingCurations
             .mergeLicenseFindingCurations(localLicenseFindingCurations, updateOnlyExisting = updateOnlyExisting)
diff --git a/helper-cli/src/main/kotlin/commands/ExportPathExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/ExportPathExcludesCommand.kt
index 2e0ba771741e4..c71cd4d591f50 100644
--- a/helper-cli/src/main/kotlin/commands/ExportPathExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ExportPathExcludesCommand.kt
@@ -71,16 +71,15 @@ internal class ExportPathExcludesCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val localPathExcludes = ortFile
-            .readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        val localPathExcludes = ortResult
             .replaceConfig(repositoryConfigurationFile)
             .getRepositoryPathExcludes()
 
-        val globalPathExcludes = if (pathExcludesFile.isFile) {
-            pathExcludesFile.readValue<RepositoryPathExcludes>()
-        } else {
-            mapOf()
-        }
+        val globalPathExcludes = pathExcludesFile.takeIf { it.isFile }?.readValue<RepositoryPathExcludes>().orEmpty()
 
         globalPathExcludes
             .mergePathExcludes(localPathExcludes, updateOnlyExisting = updateOnlyExisting)
diff --git a/helper-cli/src/main/kotlin/commands/ExtractRepositoryConfigurationCommand.kt b/helper-cli/src/main/kotlin/commands/ExtractRepositoryConfigurationCommand.kt
index 7263fda67e07a..52f239b021f10 100644
--- a/helper-cli/src/main/kotlin/commands/ExtractRepositoryConfigurationCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ExtractRepositoryConfigurationCommand.kt
@@ -50,9 +50,10 @@ class ExtractRepositoryConfigurationCommand : CliktCommand(
         .required()
 
     override fun run() {
-        ortFile
-            .readValue<OrtResult>()
-            .repository
-            .config.writeAsYaml(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        ortResult.repository.config.writeAsYaml(repositoryConfigurationFile)
     }
 }
diff --git a/helper-cli/src/main/kotlin/commands/FormatRepositoryConfigurationCommand.kt b/helper-cli/src/main/kotlin/commands/FormatRepositoryConfigurationCommand.kt
index b47fa1b638f4e..42baa04e81438 100644
--- a/helper-cli/src/main/kotlin/commands/FormatRepositoryConfigurationCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/FormatRepositoryConfigurationCommand.kt
@@ -41,8 +41,10 @@ internal class FormatRepositoryConfigurationCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        repositoryConfigurationFile
-            .readValue<RepositoryConfiguration>()
-            .writeAsYaml(repositoryConfigurationFile)
+        val repoConfig = requireNotNull(repositoryConfigurationFile.readValue<RepositoryConfiguration>()) {
+            "The provided ORT result file '${repositoryConfigurationFile.canonicalPath}' has no content."
+        }
+
+        repoConfig.writeAsYaml(repositoryConfigurationFile)
     }
 }
diff --git a/helper-cli/src/main/kotlin/commands/GenerateProjectExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/GenerateProjectExcludesCommand.kt
index 3d7613f3ff652..a8bb2c02b08d3 100644
--- a/helper-cli/src/main/kotlin/commands/GenerateProjectExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/GenerateProjectExcludesCommand.kt
@@ -57,14 +57,12 @@ internal class GenerateProjectExcludesCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val repositoryConfiguration = if (repositoryConfigurationFile.isFile) {
-            repositoryConfigurationFile.readValue()
-        } else {
-            RepositoryConfiguration()
-        }
+        val repositoryConfiguration = repositoryConfigurationFile.takeIf { it.isFile }?.readValue()
+            ?: RepositoryConfiguration()
 
-        val ortResult = ortFile.readValue<OrtResult>()
-            .replaceConfig(repositoryConfiguration)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfiguration)
 
         val generatedPathExcludes = ortResult
             .getProjects()
diff --git a/helper-cli/src/main/kotlin/commands/GenerateRuleViolationResolutionsCommand.kt b/helper-cli/src/main/kotlin/commands/GenerateRuleViolationResolutionsCommand.kt
index 6fb6f7509a551..c30ae04a19041 100644
--- a/helper-cli/src/main/kotlin/commands/GenerateRuleViolationResolutionsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/GenerateRuleViolationResolutionsCommand.kt
@@ -66,8 +66,11 @@ internal class GenerateRuleViolationResolutionsCommand : CliktCommand(
     ).enum<Severity>().split(",").default(enumValues<Severity>().asList())
 
     override fun run() {
-        val repositoryConfiguration = repositoryConfigurationFile.readValue<RepositoryConfiguration>()
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfiguration)
+        val repositoryConfiguration = repositoryConfigurationFile.readValue() ?: RepositoryConfiguration()
+
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfiguration)
 
         val generatedResolutions = ortResult
             .getUnresolvedRuleViolations()
diff --git a/helper-cli/src/main/kotlin/commands/GenerateScopeExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/GenerateScopeExcludesCommand.kt
index 07cf02330598b..ad06746d3afb7 100644
--- a/helper-cli/src/main/kotlin/commands/GenerateScopeExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/GenerateScopeExcludesCommand.kt
@@ -57,14 +57,17 @@ internal class GenerateScopeExcludesCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val scopeExcludes = ortResult.generateScopeExcludes()
 
-        repositoryConfigurationFile
-            .readValue<RepositoryConfiguration>()
-            .replaceScopeExcludes(scopeExcludes)
-            .sortScopeExcludes()
-            .writeAsYaml(repositoryConfigurationFile)
+        val repoConfig = requireNotNull(repositoryConfigurationFile.readValue<RepositoryConfiguration>()) {
+            "The provided ORT result file '${repositoryConfigurationFile.canonicalPath}' has no content."
+        }
+
+        repoConfig.replaceScopeExcludes(scopeExcludes).sortScopeExcludes().writeAsYaml(repositoryConfigurationFile)
     }
 }
 
diff --git a/helper-cli/src/main/kotlin/commands/GenerateTimeoutErrorResolutionsCommand.kt b/helper-cli/src/main/kotlin/commands/GenerateTimeoutErrorResolutionsCommand.kt
index 9325d905ae4c5..48191fc5ee396 100644
--- a/helper-cli/src/main/kotlin/commands/GenerateTimeoutErrorResolutionsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/GenerateTimeoutErrorResolutionsCommand.kt
@@ -68,13 +68,15 @@ internal class GenerateTimeoutErrorResolutionsCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfigurationFile)
 
         val resolutionProvider = DefaultResolutionProvider().apply {
             var resolutions = Resolutions()
 
-            resolutionsFile?.let {
-                resolutions = resolutions.merge(it.readValue())
+            resolutionsFile?.readValue<Resolutions>()?.let {
+                resolutions = resolutions.merge(it)
             }
 
             resolutions = resolutions.merge(ortResult.getResolutions())
diff --git a/helper-cli/src/main/kotlin/commands/ImportCopyrightGarbageCommand.kt b/helper-cli/src/main/kotlin/commands/ImportCopyrightGarbageCommand.kt
index 68a17e0a195f5..3076084cc54db 100644
--- a/helper-cli/src/main/kotlin/commands/ImportCopyrightGarbageCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ImportCopyrightGarbageCommand.kt
@@ -59,11 +59,8 @@ internal class ImportCopyrightGarbageCommand : CliktCommand(
     override fun run() {
         val entriesToImport = inputCopyrightGarbageFile.readLines().filterNot { it.isBlank() }
 
-        val existingCopyrightGarbage = if (outputCopyrightGarbageFile.isFile) {
-            outputCopyrightGarbageFile.readValue<CopyrightGarbage>().items
-        } else {
-            emptySet<String>()
-        }
+        val existingCopyrightGarbage = outputCopyrightGarbageFile.takeIf { it.isFile }
+                ?.readValue<CopyrightGarbage>()?.items.orEmpty()
 
         val collator = Collator.getInstance(Locale("en", "US.utf-8", "POSIX"))
         CopyrightGarbage((entriesToImport + existingCopyrightGarbage).toSortedSet(collator)).let {
diff --git a/helper-cli/src/main/kotlin/commands/ImportLicenseFindingCurationsCommand.kt b/helper-cli/src/main/kotlin/commands/ImportLicenseFindingCurationsCommand.kt
index f20a254200249..bd1ec5ba8b153 100644
--- a/helper-cli/src/main/kotlin/commands/ImportLicenseFindingCurationsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ImportLicenseFindingCurationsCommand.kt
@@ -76,13 +76,13 @@ internal class ImportLicenseFindingCurationsCommand : CliktCommand(
     private val findingCurationMatcher = FindingCurationMatcher()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
-        val repositoryConfiguration = if (repositoryConfigurationFile.isFile) {
-            repositoryConfigurationFile.readValue()
-        } else {
-            RepositoryConfiguration()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
         }
 
+        val repositoryConfiguration = repositoryConfigurationFile.takeIf { it.isFile }?.readValue()
+            ?: RepositoryConfiguration()
+
         val allLicenseFindings = ortResult.getLicenseFindingsForAllProjects()
 
         val importedCurations = importLicenseFindingCurations(ortResult)
@@ -102,12 +102,12 @@ internal class ImportLicenseFindingCurationsCommand : CliktCommand(
 
     private fun importLicenseFindingCurations(ortResult: OrtResult): Set<LicenseFindingCuration> {
         val repositoryPaths = ortResult.getRepositoryPaths()
-        val licenseFindingCurations = licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>()
+        val curations = licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>().orEmpty()
 
         val result = mutableSetOf<LicenseFindingCuration>()
 
         repositoryPaths.forEach { (vcsUrl, relativePaths) ->
-            licenseFindingCurations[vcsUrl]?.let { curationsForRepository ->
+            curations[vcsUrl]?.let { curationsForRepository ->
                 curationsForRepository.forEach { curation ->
                     relativePaths.forEach { path ->
                         result += curation.copy(path = path + '/' + curation.path)
diff --git a/helper-cli/src/main/kotlin/commands/ImportPathExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/ImportPathExcludesCommand.kt
index 55310090acfb6..c1e72c5a2e739 100644
--- a/helper-cli/src/main/kotlin/commands/ImportPathExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ImportPathExcludesCommand.kt
@@ -72,11 +72,8 @@ internal class ImportPathExcludesCommand : CliktCommand(
     override fun run() {
         val allFiles = findFilesRecursive(sourceCodeDir)
 
-        val repositoryConfiguration = if (repositoryConfigurationFile.isFile) {
-            repositoryConfigurationFile.readValue()
-        } else {
-            RepositoryConfiguration()
-        }
+        val repositoryConfiguration = repositoryConfigurationFile.takeIf { it.isFile }?.readValue()
+            ?: RepositoryConfiguration()
 
         val existingPathExcludes = repositoryConfiguration.excludes.paths
         val importedPathExcludes = importPathExcludes(sourceCodeDir, pathExcludesFile).filter { pathExclude ->
diff --git a/helper-cli/src/main/kotlin/commands/ImportScanResultsCommand.kt b/helper-cli/src/main/kotlin/commands/ImportScanResultsCommand.kt
index 1950d09481f9e..e7dd513e476aa 100644
--- a/helper-cli/src/main/kotlin/commands/ImportScanResultsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ImportScanResultsCommand.kt
@@ -51,7 +51,10 @@ internal class ImportScanResultsCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val scanResultsStorage = FileBasedStorage(LocalFileStorage(scanResultsStorageDir))
         val ids = ortResult.getProjects().map { it.id } + ortResult.getPackages().map { it.pkg.id }
 
diff --git a/helper-cli/src/main/kotlin/commands/ListCopyrightsCommand.kt b/helper-cli/src/main/kotlin/commands/ListCopyrightsCommand.kt
index 0f82ace73e8f1..8af1f4054999c 100644
--- a/helper-cli/src/main/kotlin/commands/ListCopyrightsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ListCopyrightsCommand.kt
@@ -88,7 +88,10 @@ internal class ListCopyrightsCommand : CliktCommand(
     ).single()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val copyrightGarbage = copyrightGarbageFile?.readValue<CopyrightGarbage>().orEmpty()
         val packageConfigurationProvider = packageConfigurationOption.createProvider()
 
diff --git a/helper-cli/src/main/kotlin/commands/ListLicenseCategoriesCommand.kt b/helper-cli/src/main/kotlin/commands/ListLicenseCategoriesCommand.kt
index cfe3446abd558..831315fb39e32 100644
--- a/helper-cli/src/main/kotlin/commands/ListLicenseCategoriesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ListLicenseCategoriesCommand.kt
@@ -48,7 +48,7 @@ class ListLicenseCategoriesCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val licenseClassifications = licenseClassificationsFile.readValue<LicenseClassifications>()
+        val licenseClassifications = licenseClassificationsFile.readValue() ?: LicenseClassifications()
 
         println(licenseClassifications.summary())
 
diff --git a/helper-cli/src/main/kotlin/commands/ListLicensesCommand.kt b/helper-cli/src/main/kotlin/commands/ListLicensesCommand.kt
index 46601cfb77535..277a918132287 100644
--- a/helper-cli/src/main/kotlin/commands/ListLicensesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ListLicensesCommand.kt
@@ -155,7 +155,9 @@ internal class ListLicensesCommand : CliktCommand(
     }.default(emptyList())
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfigurationFile)
 
         if (ortResult.getPackageOrProject(packageId) == null) {
             throw UsageError("Could not find the package for the given id '${packageId.toCoordinates()}'.")
diff --git a/helper-cli/src/main/kotlin/commands/ListPackagesCommand.kt b/helper-cli/src/main/kotlin/commands/ListPackagesCommand.kt
index 68ebd0a0e252c..8be506ddb4541 100644
--- a/helper-cli/src/main/kotlin/commands/ListPackagesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/ListPackagesCommand.kt
@@ -51,7 +51,9 @@ class ListPackagesCommand : CliktCommand(
     ).split(",").default(emptyList())
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
 
         val licenseInfoResolver = ortResult.createLicenseInfoResolver()
 
diff --git a/helper-cli/src/main/kotlin/commands/MapCopyrightsCommand.kt b/helper-cli/src/main/kotlin/commands/MapCopyrightsCommand.kt
index f8c5427700fbe..155e8f3f50a01 100644
--- a/helper-cli/src/main/kotlin/commands/MapCopyrightsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/MapCopyrightsCommand.kt
@@ -61,9 +61,11 @@ internal class MapCopyrightsCommand : CliktCommand(
     override fun run() {
         val processedCopyrightStatements = inputCopyrightGarbageFile.readLines().filterNot { it.isBlank() }
 
-        val unprocessedCopyrightStatements = ortFile
-            .readValue<OrtResult>()
-            .getUnprocessedCopyrightStatements(processedCopyrightStatements)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        val unprocessedCopyrightStatements = ortResult.getUnprocessedCopyrightStatements(processedCopyrightStatements)
 
         outputCopyrightsFile.writeText(unprocessedCopyrightStatements.joinToString(separator = "\n"))
     }
diff --git a/helper-cli/src/main/kotlin/commands/MergeRepositoryConfigurationsCommand.kt b/helper-cli/src/main/kotlin/commands/MergeRepositoryConfigurationsCommand.kt
index b190b800a5486..c4527b64ec7cf 100644
--- a/helper-cli/src/main/kotlin/commands/MergeRepositoryConfigurationsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/MergeRepositoryConfigurationsCommand.kt
@@ -55,7 +55,7 @@ internal class MergeRepositoryConfigurationsCommand : CliktCommand(
         var result = RepositoryConfiguration()
 
         inputRepositoryConfigurationFiles.forEach { file ->
-            val repositoryConfiguration = file.readValue<RepositoryConfiguration>()
+            val repositoryConfiguration = file.readValue() ?: RepositoryConfiguration()
             result = result.merge(repositoryConfiguration)
         }
 
diff --git a/helper-cli/src/main/kotlin/commands/RemoveConfigurationEntriesCommand.kt b/helper-cli/src/main/kotlin/commands/RemoveConfigurationEntriesCommand.kt
index f93c4c33ae2b9..fd741f74b3aca 100644
--- a/helper-cli/src/main/kotlin/commands/RemoveConfigurationEntriesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/RemoveConfigurationEntriesCommand.kt
@@ -78,8 +78,11 @@ internal class RemoveConfigurationEntriesCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        val repositoryConfiguration = repositoryConfigurationFile.readValue<RepositoryConfiguration>()
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfiguration)
+        val repositoryConfiguration = repositoryConfigurationFile.readValue() ?: RepositoryConfiguration()
+
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfiguration)
 
         val pathExcludes = findFilesRecursive(sourceCodeDir).let { allFiles ->
             ortResult.getExcludes().paths.filter { pathExclude ->
diff --git a/helper-cli/src/main/kotlin/commands/SortRepositoryConfigurationCommand.kt b/helper-cli/src/main/kotlin/commands/SortRepositoryConfigurationCommand.kt
index 3080199319d8f..ac28580690317 100644
--- a/helper-cli/src/main/kotlin/commands/SortRepositoryConfigurationCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/SortRepositoryConfigurationCommand.kt
@@ -42,9 +42,7 @@ internal class SortRepositoryConfigurationCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        repositoryConfigurationFile
-            .readValue<RepositoryConfiguration>()
-            .sortEntries()
-            .writeAsYaml(repositoryConfigurationFile)
+        repositoryConfigurationFile.readValue<RepositoryConfiguration>()
+            ?.sortEntries()?.writeAsYaml(repositoryConfigurationFile)
     }
 }
diff --git a/helper-cli/src/main/kotlin/commands/SubtractScanResultsCommand.kt b/helper-cli/src/main/kotlin/commands/SubtractScanResultsCommand.kt
index 39f3b1b87400f..8c441bfa86f33 100644
--- a/helper-cli/src/main/kotlin/commands/SubtractScanResultsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/SubtractScanResultsCommand.kt
@@ -64,15 +64,28 @@ internal class SubtractScanResultsCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val lhsOrtResult = lhsOrtFile.readValue<OrtResult>()
-        val rhsOrtResult = rhsOrtFile.readValue<OrtResult>()
+        val lhsOrtResult = requireNotNull(lhsOrtFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${lhsOrtFile.canonicalPath}' has no content."
+        }
+
+        val lhsScannerRun = requireNotNull(lhsOrtResult.scanner) {
+            "The ORT result file '${lhsOrtFile.canonicalPath}' does not contain a scanner run."
+        }
+
+        val rhsOrtResult = requireNotNull(rhsOrtFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${rhsOrtFile.canonicalPath}' has no content."
+        }
+
+        val rhsScannerRun = requireNotNull(rhsOrtResult.scanner) {
+            "The ORT result file '${rhsOrtFile.canonicalPath}' does not contain a scanner run."
+        }
 
-        val rhsScanSummaries = rhsOrtResult.scanner!!.results.scanResults.flatMap { it.value }.associateBy(
+        val rhsScanSummaries = rhsScannerRun.results.scanResults.flatMap { it.value }.associateBy(
             keySelector = { it.provenance.key() },
             valueTransform = { it.summary }
         )
 
-        val scanResults = lhsOrtResult.scanner!!.results.scanResults.mapValuesTo(sortedMapOf()) { (_, results) ->
+        val scanResults = lhsScannerRun.results.scanResults.mapValuesTo(sortedMapOf()) { (_, results) ->
             results.map { lhsScanResult ->
                 val lhsSummary = lhsScanResult.summary
                 val rhsSummary = rhsScanSummaries[lhsScanResult.provenance.key()]
@@ -82,8 +95,8 @@ internal class SubtractScanResultsCommand : CliktCommand(
         }
 
        val result = lhsOrtResult.copy(
-           scanner = lhsOrtResult.scanner!!.copy(
-               results = lhsOrtResult.scanner!!.results.copy(
+           scanner = lhsScannerRun.copy(
+               results = lhsScannerRun.results.copy(
                     scanResults = scanResults
                )
            )
diff --git a/helper-cli/src/main/kotlin/commands/VerifySourceArtifactCurationsCommand.kt b/helper-cli/src/main/kotlin/commands/VerifySourceArtifactCurationsCommand.kt
index b004ac1cf2b90..217aecf89623e 100644
--- a/helper-cli/src/main/kotlin/commands/VerifySourceArtifactCurationsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/VerifySourceArtifactCurationsCommand.kt
@@ -44,7 +44,7 @@ internal class VerifySourceArtifactCurationsCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        val curations = packageCurationsFile.readValue<List<PackageCuration>>()
+        val curations = packageCurationsFile.readValue<List<PackageCuration>>().orEmpty()
 
         val failed = curations.filterNot { curation ->
             curation.data.sourceArtifact?.let { sourceArtifact ->
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/ExportPathExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/ExportPathExcludesCommand.kt
index b07c3b8bcc7e0..087f0add8031d 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/ExportPathExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/ExportPathExcludesCommand.kt
@@ -69,14 +69,10 @@ class ExportPathExcludesCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val globalPathExcludes = if (pathExcludesFile.isFile) {
-            pathExcludesFile.readValue<RepositoryPathExcludes>()
-        } else {
-            mapOf()
-        }
+        val globalPathExcludes = pathExcludesFile.takeIf { it.isFile }?.readValue<RepositoryPathExcludes>().orEmpty()
 
         val localPathExcludes = getPathExcludesByRepository(
-            pathExcludes = packageConfigurationFile.readValue<PackageConfiguration>().pathExcludes,
+            pathExcludes = packageConfigurationFile.readValue<PackageConfiguration>()?.pathExcludes.orEmpty(),
             nestedRepositories = findRepositories(sourceCodeDir)
         )
 
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/FindCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/FindCommand.kt
index cdf0240b8d2d4..90c8182a46b17 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/FindCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/FindCommand.kt
@@ -52,7 +52,7 @@ internal class FindCommand : CliktCommand(
     override fun run() {
         // TODO: There could be multiple package configurations matching the given identifier which is not handled.
         findPackageConfigurationFiles(packageConfigurationDir).find {
-            it.readValue<PackageConfiguration>().id == packageId
+            it.readValue<PackageConfiguration>()?.id == packageId
         }?.let {
             println(it.absolutePath)
         }
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/FormatCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/FormatCommand.kt
index 0572d157ef66c..e77c343f28518 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/FormatCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/FormatCommand.kt
@@ -41,8 +41,6 @@ internal class FormatCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        packageConfigurationFile
-            .readValue<PackageConfiguration>()
-            .writeAsYaml(packageConfigurationFile)
+        packageConfigurationFile.readValue<PackageConfiguration>()?.writeAsYaml(packageConfigurationFile)
     }
 }
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/ImportLicenseFindingCurationsCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/ImportLicenseFindingCurationsCommand.kt
index 2fe3afec6d648..361c69969ca70 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/ImportLicenseFindingCurationsCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/ImportLicenseFindingCurationsCommand.kt
@@ -82,8 +82,13 @@ class ImportLicenseFindingCurationsCommand : CliktCommand(
     private val findingCurationMatcher = FindingCurationMatcher()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
-        val packageConfiguration = packageConfigurationFile.readValue<PackageConfiguration>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        val packageConfiguration = requireNotNull(packageConfigurationFile.readValue<PackageConfiguration>()) {
+            "The provided package configuration file '${packageConfigurationFile.canonicalPath}' has no content."
+        }
 
         val allLicenseFindings = ortResult.getScanResultFor(packageConfiguration)?.summary?.licenseFindings.orEmpty()
 
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/ImportPathExcludesCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/ImportPathExcludesCommand.kt
index 06a131bb3a3f0..959d4e77a73b8 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/ImportPathExcludesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/ImportPathExcludesCommand.kt
@@ -70,7 +70,9 @@ class ImportPathExcludesCommand : CliktCommand(
     override fun run() {
         val allFiles = findFilesRecursive(sourceCodeDir)
 
-        val packageConfiguration = packageConfigurationFile.readValue<PackageConfiguration>()
+        val packageConfiguration = requireNotNull(packageConfigurationFile.readValue<PackageConfiguration>()) {
+            "The provided package configuration file '${packageConfigurationFile.canonicalPath}' has no content."
+        }
 
         val existingPathExcludes = packageConfiguration.pathExcludes
         val importedPathExcludes = importPathExcludes(sourceCodeDir, pathExcludesFile).filter { pathExclude ->
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/RemoveEntriesCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/RemoveEntriesCommand.kt
index 8ec371e325f79..d8c37dbdf2aeb 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/RemoveEntriesCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/RemoveEntriesCommand.kt
@@ -57,8 +57,14 @@ internal class RemoveEntriesCommand : CliktCommand(
     private val findingsMatcher = FindingCurationMatcher()
 
     override fun run() {
-        val packageConfiguration = packageConfigurationFile.readValue<PackageConfiguration>()
-        val ortResult = ortFile.readValue<OrtResult>()
+        val packageConfiguration = requireNotNull(packageConfigurationFile.readValue<PackageConfiguration>()) {
+            "The provided package configuration file '${packageConfigurationFile.canonicalPath}' has no content."
+        }
+
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val scanResult = ortResult.getScanResultFor(packageConfiguration)
 
         if (scanResult == null) {
diff --git a/helper-cli/src/main/kotlin/commands/packageconfig/SortCommand.kt b/helper-cli/src/main/kotlin/commands/packageconfig/SortCommand.kt
index 6701dc6cd3e5b..308a570488d80 100644
--- a/helper-cli/src/main/kotlin/commands/packageconfig/SortCommand.kt
+++ b/helper-cli/src/main/kotlin/commands/packageconfig/SortCommand.kt
@@ -42,9 +42,6 @@ internal class SortCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        packageConfigurationFile
-            .readValue<PackageConfiguration>()
-            .sortEntries()
-            .writeAsYaml(packageConfigurationFile)
+        packageConfigurationFile.readValue<PackageConfiguration>()?.sortEntries()?.writeAsYaml(packageConfigurationFile)
     }
 }
diff --git a/helper-cli/src/main/kotlin/common/Utils.kt b/helper-cli/src/main/kotlin/common/Utils.kt
index c93ae64db531e..20a828e399fd8 100644
--- a/helper-cli/src/main/kotlin/common/Utils.kt
+++ b/helper-cli/src/main/kotlin/common/Utils.kt
@@ -809,7 +809,7 @@ internal fun importPathExcludes(sourceCodeDir: File, pathExcludesFile: File): Li
     println("Found ${repositoryPaths.size} repositories in ${repositoryPaths.values.sumBy { it.size }} locations.")
 
     println("Loading $pathExcludesFile...")
-    val pathExcludes = pathExcludesFile.readValue<RepositoryPathExcludes>()
+    val pathExcludes = pathExcludesFile.readValue<RepositoryPathExcludes>().orEmpty()
     println("Found ${pathExcludes.values.sumBy { it.size }} excludes for ${pathExcludes.size} repositories.")
 
     val result = mutableListOf<PathExclude>()
@@ -836,7 +836,7 @@ internal fun importLicenseFindingCurations(
     println("Found ${repositoryPaths.size} repositories in ${repositoryPaths.values.sumBy { it.size }} locations.")
 
     println("Loading $licenseFindingCurationsFile...")
-    val curations = licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>()
+    val curations = licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>().orEmpty()
     println("Found ${curations.values.sumBy { it.size }} curations for ${curations.size} repositories.")
 
     val result = mutableListOf<LicenseFindingCuration>()
diff --git a/model/src/main/kotlin/FileFormat.kt b/model/src/main/kotlin/FileFormat.kt
index ee006ac87a02f..c757e95bc50ba 100644
--- a/model/src/main/kotlin/FileFormat.kt
+++ b/model/src/main/kotlin/FileFormat.kt
@@ -20,7 +20,7 @@
 package org.ossreviewtoolkit.model
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import com.fasterxml.jackson.module.kotlin.readValue
+import com.fasterxml.jackson.module.kotlin.treeToValue
 
 import java.io.File
 
@@ -77,6 +77,12 @@ enum class FileFormat(val mapper: ObjectMapper, val fileExtension: String, varar
 fun File.mapper() = FileFormat.forFile(this).mapper
 
 /**
- * Use the Jackson mapper returned from [File.mapper] to read an object of type [T] from this file.
+ * Use the Jackson mapper returned from [File.mapper] to read an object of type [T] from this file, or return null if
+ * the file has no content.
  */
-inline fun <reified T : Any> File.readValue(): T = mapper().readValue(this)
+inline fun <reified T : Any> File.readValue(): T? =
+    mapper().readTree(this)?.let {
+        // Parse the file in a two-step process to avoid readValue() throwing an exception on empty files. Also see
+        // https://github.com/FasterXML/jackson-databind/issues/1406#issuecomment-252676674.
+        mapper().treeToValue(it)
+    }
diff --git a/model/src/main/kotlin/utils/SimplePackageConfigurationProvider.kt b/model/src/main/kotlin/utils/SimplePackageConfigurationProvider.kt
index f3e758734a332..ae70baf9bd292 100644
--- a/model/src/main/kotlin/utils/SimplePackageConfigurationProvider.kt
+++ b/model/src/main/kotlin/utils/SimplePackageConfigurationProvider.kt
@@ -48,7 +48,7 @@ class SimplePackageConfigurationProvider(
          * configuration per [Identifier] and [Provenance].
          */
         fun forDirectory(directory: File): SimplePackageConfigurationProvider {
-            val entries = findPackageConfigurationFiles(directory).mapTo(mutableListOf()) { file ->
+            val entries = findPackageConfigurationFiles(directory).mapNotNullTo(mutableListOf()) { file ->
                 try {
                     file.readValue<PackageConfiguration>()
                 } catch (e: IOException) {
@@ -67,7 +67,7 @@ class SimplePackageConfigurationProvider(
          * file. Throws an exception if there is more than one configuration per [Identifier] and [Provenance].
          */
         fun forFile(file: File): SimplePackageConfigurationProvider {
-            val entries = file.readValue<List<PackageConfiguration>>()
+            val entries = file.readValue<List<PackageConfiguration>>().orEmpty()
 
             return SimplePackageConfigurationProvider(entries)
         }
diff --git a/model/src/test/kotlin/AdvisorResultContainerTest.kt b/model/src/test/kotlin/AdvisorResultContainerTest.kt
index 64d883be1af08..b5bc7136a3323 100644
--- a/model/src/test/kotlin/AdvisorResultContainerTest.kt
+++ b/model/src/test/kotlin/AdvisorResultContainerTest.kt
@@ -99,7 +99,7 @@ class AdvisorResultContainerTest : WordSpec() {
 
                 val result = resultsFile.readValue<OrtResult>()
 
-                result.advisor shouldNot beNull()
+                result?.advisor shouldNot beNull()
             }
 
             "be deserialized with vulnerabilities in format with references" {
@@ -107,7 +107,7 @@ class AdvisorResultContainerTest : WordSpec() {
 
                 val result = resultsFile.readValue<OrtResult>()
 
-                result.advisor shouldNot beNull()
+                result?.advisor shouldNot beNull()
             }
         }
     }
diff --git a/model/src/test/kotlin/ProjectTest.kt b/model/src/test/kotlin/ProjectTest.kt
index 76c4cb991be4d..2628c934cd2ee 100644
--- a/model/src/test/kotlin/ProjectTest.kt
+++ b/model/src/test/kotlin/ProjectTest.kt
@@ -39,7 +39,7 @@ import org.ossreviewtoolkit.utils.test.containExactly
 private fun readAnalyzerResult(analyzerResultFilename: String): Project =
     File("../analyzer/src/funTest/assets/projects/synthetic")
         .resolve(analyzerResultFilename)
-        .readValue<ProjectAnalyzerResult>().project
+        .readValue<ProjectAnalyzerResult>()?.project ?: Project.EMPTY
 
 private const val MANAGER = "MyManager"
 
diff --git a/model/src/test/kotlin/config/NexusIqConfigurationTest.kt b/model/src/test/kotlin/config/NexusIqConfigurationTest.kt
index 562d20a81c4bb..f34b23beffdc9 100644
--- a/model/src/test/kotlin/config/NexusIqConfigurationTest.kt
+++ b/model/src/test/kotlin/config/NexusIqConfigurationTest.kt
@@ -40,7 +40,7 @@ class NexusIqConfigurationTest : WordSpec({
             }.readValue<OrtConfiguration>()
 
             val expectedNexusIqConfig = referenceOrtConfig.advisor.nexusIq
-            val actualNexusIqConfiguration = rereadOrtConfig.advisor.nexusIq
+            val actualNexusIqConfiguration = rereadOrtConfig?.advisor?.nexusIq
 
             expectedNexusIqConfig.shouldBeInstanceOf<NexusIqConfiguration>()
             actualNexusIqConfiguration.shouldBeInstanceOf<NexusIqConfiguration>()
diff --git a/model/src/test/kotlin/config/ScannerConfigurationTest.kt b/model/src/test/kotlin/config/ScannerConfigurationTest.kt
index 285bf98537732..6b5ab84746a5e 100644
--- a/model/src/test/kotlin/config/ScannerConfigurationTest.kt
+++ b/model/src/test/kotlin/config/ScannerConfigurationTest.kt
@@ -40,7 +40,7 @@ class ScannerConfigurationTest : WordSpec({
             val file = createTempFile(suffix = ".yml").toFile().apply { deleteOnExit() }
 
             file.mapper().writeValue(file, ortConfig.scanner)
-            val loadedConfig = file.readValue<ScannerConfiguration>()
+            val loadedConfig = file.readValue() ?: ScannerConfiguration()
 
             // Note: loadedConfig cannot be directly compared to the original one, as there have been some changes:
             // Relative paths have been normalized, passwords do not get serialized, etc.
diff --git a/scanner/src/main/kotlin/Scanner.kt b/scanner/src/main/kotlin/Scanner.kt
index a1dd59e2b212e..1c518cd461be3 100644
--- a/scanner/src/main/kotlin/Scanner.kt
+++ b/scanner/src/main/kotlin/Scanner.kt
@@ -108,8 +108,16 @@ abstract class Scanner(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
-        requireNotNull(ortResult.analyzer) {
-            "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        if (ortResult.analyzer == null) {
+            log.warn {
+                "The provided ORT result file '${ortFile.canonicalPath}' does not contain an analyzer result."
+            }
+
+            return ortResult
         }
 
         // Add the projects as packages to scan.