Sync more than one source directory into a single bucket/prefix (#25)

* [changelog] updated

* [readme] updated

* [core] ConfigQuery added sources()

* [cli] ParseArgs allow specifying multiple sources

* [domain,core,cli] Source datatype changed to Path

* [domain] Sources added to hold multiple paths in order

* [domain] Config sources change datatype to Sources

* [core] Scan sources for .thorp.config and include any sources listed

This allows the inclusion of a `.thorp.config` file in a source with a
single line `source = ....` that causes that other source to also be
synched into the same remote prefix as the current source.

* [core] ConfigurationBuilderTest add more pending tests

* [[core] ConfigurationBuilderTest rewrite using loan-pattern for fixtures

* [core] ConfigOptionTest use TemporaryFolder

* [core] ConfigOptionTest remove unused fields

* [cli] ParseArgsTest don't use get on an Option

* [core] ConfigurationBuilderTest don't use get on Either

* [core] TemporaryFolder Move import to top of file

* [core] TemporaryFolder use Try over try-finally

* [core] ConfigurationBuilderTest don't use get on Either

* [core] TemporaryFolders.withDirectory propogate errors

* [core] TemporaryFolders add writeFile and createFile

* [core] PlanBuilderTest create a plan with two sources with unique files in both

* [core] ActionGenerator only upload file by name in first source

create a plan
  two sources
    same filename in both
    - only upload file in first source

* [domain] LastModified with no params is now()

* [core] PlanBuilderTest 2 sources w/remote only in 2nd src do nothing

* [core] PlanBuilderTest 2 sources w/remote only in 2nd src do nothing

* [domain] RemoteKey map to a file when prefix is empty

* [domain] S3ObjectData defaults to empty

* [core] KeyGenerator Avoid delimiter when empty prefix key

* [core] PlanBuilderTest when remote not in sources delete from remote

* [core] PlanBuilderTest extract helper md5Hash()

* [core] PlanBuilderTest one source a file no matching remote key

* [core] PlanBuildingTest file with matching key and hash do nothing

* [core] PlanBuilderTest file w/matching remote key and different hash

* [core] PlanBuilderTest a remote key with and without local file

* [core] DummyStorageService Use wildcards when selecting more than 6 elements

CHANGELOG.org

@@ -12,6 +12,7 @@ The format is based on [[https://keepachangelog.com/en/1.0.0/][Keep a Changelog]
    - Add a version command-line option (#99)
    - Add a batch mode (#85)
    - Display total size and progress for entire run (#94)
+   - Sync more than one source directory into a single bucket/prefile (#25)
 
 * [0.6.1] - 2019-07-03
 

README.org

@@ -33,6 +33,10 @@ If you don't provide a ~source~ the current diretory will be used.
 
 The ~--include~ and ~--exclude~ parameters can be used more than once.
 
+The ~--source~ parameter can be used more than once, in which case,
+all files in all sources will be consolidated into the same
+bucket/prefix.
+
 ** Batch mode
 
 Batch mode disable the ANSI console display and logs simple messages
@@ -46,15 +50,18 @@ that can be written to a file.
   - User: ~ ~/.config/thorp.conf~
   - Source: ~${source}/.thorp.conf~
 
-Command line arguments override those in Source, which override those
+  Command line arguments override those in Source, which override
-in User, which override those Global, which override any built-in
+  those in User, which override those Global, which override any
-config.
+  built-in config.
 
-Built-in config consists of using the current working directory as the
+  When there is more than one source, only the first ".thorp.conf"
-~source~.
+  file found will be used.
 
-Note, that ~include~ and ~exclude~ are cumulative across all
+  Built-in config consists of using the current working directory as
-configuration files.
+  the ~source~.
+
+  Note, that ~include~ and ~exclude~ are cumulative across all
+  configuration files.
 
 * Behaviour
 

cli/src/main/scala/net/kemitix/thorp/cli/ParseArgs.scala

@@ -20,6 +20,7 @@ object ParseArgs {
         .action((_, cos) => ConfigOption.BatchMode :: cos)
         .text("Enable batch-mode"),
       opt[String]('s', "source")
+        .unbounded()
         .action((str, cos) => ConfigOption.Source(Paths.get(str)) :: cos)
         .text("Source directory to sync to destination"),
       opt[String]('b', "bucket")

cli/src/test/scala/net/kemitix/thorp/cli/ParseArgsTest.scala

@@ -1,7 +1,9 @@
 package net.kemitix.thorp.cli
 
+import java.nio.file.Paths
+
 import net.kemitix.thorp.core.ConfigOption.Debug
-import net.kemitix.thorp.core.{ConfigOptions, Resource}
+import net.kemitix.thorp.core.{ConfigOptions, ConfigQuery, Resource}
 import org.scalatest.FunSpec
 
 import scala.util.Try
@@ -15,14 +17,27 @@ class ParseArgsTest extends FunSpec {
       ParseArgs(List("--source", path, "--bucket", "bucket"))
 
     describe("when source is a directory") {
-      val result = invokeWithSource(pathTo("."))
       it("should succeed") {
+        val result = invokeWithSource(pathTo("."))
         assert(result.isDefined)
       }
     }
     describe("when source is a relative path to a directory") {
+      val result = invokeWithSource(pathTo("."))
       it("should succeed") {pending}
     }
+    describe("when there are multiple sources") {
+      val args = List(
+        "--source", "path1",
+        "--source", "path2",
+        "--bucket", "bucket")
+      it("should get multiple sources") {
+        val expected = Some(Set("path1", "path2").map(Paths.get(_)))
+        val configOptions = ParseArgs(args)
+        val result = configOptions.map(ConfigQuery.sources(_).paths.toSet)
+        assertResult(expected)(result)
+      }
+    }
   }
 
   describe("parse - debug") {

cli/src/test/scala/net/kemitix/thorp/cli/ProgramTest.scala

@@ -1,22 +1,24 @@
 package net.kemitix.thorp.cli
 
 import java.io.File
+import java.nio.file.Path
 
 import cats.data.EitherT
 import cats.effect.IO
 import net.kemitix.thorp.core.Action.{ToCopy, ToDelete, ToUpload}
 import net.kemitix.thorp.core._
-import net.kemitix.thorp.domain.{Bucket, LocalFile, Logger, MD5Hash, RemoteKey, StorageQueueEvent}
+import net.kemitix.thorp.domain._
 import net.kemitix.thorp.storage.api.{HashService, StorageService}
 import org.scalatest.FunSpec
 
 class ProgramTest extends FunSpec {
 
   val source: File = Resource(this, ".")
+  val sourcePath: Path = source.toPath
   val bucket: Bucket = Bucket("aBucket")
   val hash: MD5Hash = MD5Hash("aHash")
   val copyAction: Action = ToCopy(bucket, RemoteKey("copy-me"), hash, RemoteKey("overwrite-me"), 17L)
-  val uploadAction: Action = ToUpload(bucket, LocalFile.resolve("aFile", Map(), source, _ => RemoteKey("upload-me")), 23L)
+  val uploadAction: Action = ToUpload(bucket, LocalFile.resolve("aFile", Map(), sourcePath, _ => RemoteKey("upload-me")), 23L)
   val deleteAction: Action = ToDelete(bucket, RemoteKey("delete-me"), 0L)
 
   val configOptions: ConfigOptions = ConfigOptions(options = List(

core/src/main/scala/net/kemitix/thorp/core/ActionGenerator.scala

@@ -5,7 +5,17 @@ import net.kemitix.thorp.domain._
 
 object ActionGenerator {
 
-  def createActions(s3MetaData: S3MetaData)
+  def remoteNameNotAlreadyQueued(localFile: LocalFile,
+                                 previousActions: Stream[Action]): Boolean = {
+    val key = localFile.remoteKey.key
+    !previousActions.exists {
+      case ToUpload(_, lf, _) => lf.remoteKey.key equals key
+      case _ => false
+    }
+  }
+
+  def createActions(s3MetaData: S3MetaData,
+                    previousActions: Stream[Action])
                    (implicit c: Config): Stream[Action] =
     s3MetaData match {
 
@@ -21,7 +31,8 @@ object ActionGenerator {
 
       // #3 local exists, remote is missing, other no matches - upload
       case S3MetaData(localFile, otherMatches, None)
-        if otherMatches.isEmpty
+        if otherMatches.isEmpty &&
+          remoteNameNotAlreadyQueued(localFile, previousActions)
       => uploadFile(c.bucket, localFile)
 
       // #4 local exists, remote exists, remote no match, other matches - copy
@@ -35,6 +46,8 @@ object ActionGenerator {
         if hashMatches.isEmpty
       => uploadFile(c.bucket, localFile)
 
+      case S3MetaData(localFile, _, _) =>
+        doNothing(c.bucket, localFile.remoteKey)
     }
 
   private def doNothing(bucket: Bucket,

core/src/main/scala/net/kemitix/thorp/core/ConfigOption.scala

@@ -17,13 +17,21 @@ object ConfigOption {
     override def update(config: Config): Config = config.copy(batchMode = true)
   }
   case class Source(path: Path) extends ConfigOption {
-    override def update(config: Config): Config = config.copy(source = path.toFile)
+    override def update(config: Config): Config = config.copy(sources = config.sources ++ path)
   }
   case class Bucket(name: String) extends ConfigOption {
-    override def update(config: Config): Config = config.copy(bucket = domain.Bucket(name))
+    override def update(config: Config): Config =
+      if (config.bucket.name.isEmpty)
+        config.copy(bucket = domain.Bucket(name))
+      else
+        config
   }
   case class Prefix(path: String) extends ConfigOption {
-    override def update(config: Config): Config = config.copy(prefix = RemoteKey(path))
+    override def update(config: Config): Config =
+      if (config.prefix.key.isEmpty)
+        config.copy(prefix = RemoteKey(path))
+      else
+        config
   }
   case class Include(pattern: String) extends ConfigOption {
     override def update(config: Config): Config = config.copy(filters = domain.Filter.Include(pattern) :: config.filters)

core/src/main/scala/net/kemitix/thorp/core/ConfigQuery.scala

@@ -1,5 +1,7 @@
 package net.kemitix.thorp.core
 
+import net.kemitix.thorp.domain.Sources
+
 trait ConfigQuery {
 
   def showVersion(configOptions: ConfigOptions): Boolean =
@@ -14,6 +16,13 @@ trait ConfigQuery {
   def ignoreGlobalOptions(configOptions: ConfigOptions): Boolean =
     configOptions contains ConfigOption.IgnoreGlobalOptions
 
+  def sources(configOptions: ConfigOptions): Sources = {
+    val paths = configOptions.options.flatMap( {
+      case ConfigOption.Source(sourcePath) => Some(sourcePath)
+      case _ => None
+    })
+    Sources(paths)
+  }
 }
 
 object ConfigQuery extends ConfigQuery

core/src/main/scala/net/kemitix/thorp/core/ConfigValidator.scala

@@ -1,33 +1,40 @@
 package net.kemitix.thorp.core
 
-import java.io.File
+import java.nio.file.Path
 
 import cats.data.{NonEmptyChain, Validated, ValidatedNec}
 import cats.implicits._
-import net.kemitix.thorp.domain.{Bucket, Config}
+import net.kemitix.thorp.domain.{Bucket, Config, Sources}
 
 sealed trait ConfigValidator {
 
   type ValidationResult[A] = ValidatedNec[ConfigValidation, A]
 
-  def validateSourceIsDirectory(source: File): ValidationResult[File] =
+  def validateSourceIsDirectory(source: Path): ValidationResult[Path] =
-    if(source.isDirectory) source.validNec
+    if(source.toFile.isDirectory) source.validNec
     else ConfigValidation.SourceIsNotADirectory.invalidNec
 
-  def validateSourceIsReadable(source: File): ValidationResult[File] =
+  def validateSourceIsReadable(source: Path): ValidationResult[Path] =
-    if(source.canRead) source.validNec
+    if(source.toFile.canRead) source.validNec
     else ConfigValidation.SourceIsNotReadable.invalidNec
 
-  def validateSource(source: File): ValidationResult[File] =
+  def validateSource(source: Path): ValidationResult[Path] =
-    validateSourceIsDirectory(source).andThen(s => validateSourceIsReadable(s))
+    validateSourceIsDirectory(source)
+      .andThen(s =>
+        validateSourceIsReadable(s))
 
   def validateBucket(bucket: Bucket): ValidationResult[Bucket] =
     if (bucket.name.isEmpty) ConfigValidation.BucketNameIsMissing.invalidNec
     else bucket.validNec
 
+  def validateSources(sources: Sources): ValidationResult[Sources] =
+    sources.paths
+      .map(validateSource).sequence
+      .map(_ => sources)
+
   def validateConfig(config: Config): Validated[NonEmptyChain[ConfigValidation], Config] =
     (
-      validateSource(config.source),
+      validateSources(config.sources),
       validateBucket(config.bucket)
     ).mapN((_, _) => config)
 }

core/src/main/scala/net/kemitix/thorp/core/ConfigurationBuilder.scala

@@ -1,13 +1,13 @@
 package net.kemitix.thorp.core
 
-import java.io.File
+import java.nio.file.{Files, Path, Paths}
-import java.nio.file.Paths
 
 import cats.data.NonEmptyChain
 import cats.effect.IO
+import cats.implicits._
 import net.kemitix.thorp.core.ConfigValidator.validateConfig
 import net.kemitix.thorp.core.ParseConfigFile.parseFile
-import net.kemitix.thorp.domain.Config
+import net.kemitix.thorp.domain.{Config, Sources}
 
 /**
   * Builds a configuration from settings in a file within the
@@ -15,14 +15,11 @@ import net.kemitix.thorp.domain.Config
   */
 trait ConfigurationBuilder {
 
-  private val pwdFile: File = Paths.get(System.getenv("PWD")).toFile
-
-  private val defaultConfig: Config = Config(source = pwdFile)
 
   def buildConfig(priorityOptions: ConfigOptions): IO[Either[NonEmptyChain[ConfigValidation], Config]] = {
-    val source = findSource(priorityOptions)
+    val sources = ConfigQuery.sources(priorityOptions)
     for {
-      sourceOptions <- sourceOptions(source)
+      sourceOptions <- sourceOptions(sources)
       userOptions <- userOptions(priorityOptions ++ sourceOptions)
       globalOptions <- globalOptions(priorityOptions ++ sourceOptions ++ userOptions)
       collected = priorityOptions ++ sourceOptions ++ userOptions ++ globalOptions
@@ -30,14 +27,39 @@ trait ConfigurationBuilder {
     } yield validateConfig(config).toEither
   }
 
-  private def findSource(priorityOptions: ConfigOptions): File =
+  private def sourceOptions(sources: Sources): IO[ConfigOptions] = {
-    priorityOptions.options.foldRight(pwdFile)((co, f) => co match {
+    def existingThorpConfigFiles(sources: Sources) =
-      case ConfigOption.Source(source) => source.toFile
+      sources.paths
-      case _ => f
+        .map(_.resolve(".thorp.config"))
-    })
+        .filter(Files.exists(_))
 
-  private def sourceOptions(source: File): IO[ConfigOptions] =
+    def filterForSources: IO[ConfigOptions] => IO[(Sources, ConfigOptions)] =
-    readFile(source, ".thorp.conf")
+      for {configOptions <- _} yield (ConfigQuery.sources(configOptions), configOptions)
+
+    def recurseIntoSources: IO[(Sources, ConfigOptions)] => IO[ConfigOptions] =
+      ioSourcesConfigOptions =>
+        for {
+          sourcesConfigOptions <- ioSourcesConfigOptions
+          (sources, configOptions) = sourcesConfigOptions
+          moreSourcesConfigOptions <- filterForSources(sourceOptions(sources))
+          (_, moreConfigOptions) = moreSourcesConfigOptions
+        } yield configOptions ++ moreConfigOptions
+
+    def emptyConfig: IO[ConfigOptions] = IO.pure(ConfigOptions())
+
+    def collectConfigOptions: (IO[ConfigOptions], IO[ConfigOptions]) => IO[ConfigOptions] =
+      (ioConfigOptions, ioAcc) =>
+        for {
+          configOptions <- ioConfigOptions
+          acc <- ioAcc
+        } yield configOptions ++ acc
+
+    existingThorpConfigFiles(sources)
+      .map(ParseConfigFile.parseFile)
+      .map(filterForSources)
+      .map(recurseIntoSources)
+      .foldRight(emptyConfig)(collectConfigOptions)
+  }
 
   private def userOptions(higherPriorityOptions: ConfigOptions): IO[ConfigOptions] =
     if (ConfigQuery.ignoreUserOptions(higherPriorityOptions)) IO(ConfigOptions())
@@ -47,13 +69,22 @@ trait ConfigurationBuilder {
     if (ConfigQuery.ignoreGlobalOptions(higherPriorityOptions)) IO(ConfigOptions())
     else parseFile(Paths.get("/etc/thorp.conf"))
 
-  private def userHome = new File(System.getProperty("user.home"))
+  private def userHome = Paths.get(System.getProperty("user.home"))
 
-  private def readFile(source: File, filename: String): IO[ConfigOptions] =
+  private def readFile(source: Path, filename: String): IO[ConfigOptions] =
-    parseFile(source.toPath.resolve(filename))
+    parseFile(source.resolve(filename))
 
-  private def collateOptions(configOptions: ConfigOptions): Config =
+  private def collateOptions(configOptions: ConfigOptions): Config = {
-    configOptions.options.foldRight(defaultConfig)((co, c) => co.update(c))
+    val pwd = Paths.get(System.getenv("PWD"))
+    val initialSource =
+      if (noSourcesProvided(configOptions)) List(pwd) else List()
+    val initialConfig = Config(sources = Sources(initialSource))
+    configOptions.options.foldLeft(initialConfig)((c, co) => co.update(c))
+  }
+
+  private def noSourcesProvided(configOptions: ConfigOptions) = {
+    ConfigQuery.sources(configOptions).paths.isEmpty
+  }
 }
 
 object ConfigurationBuilder extends ConfigurationBuilder

core/src/main/scala/net/kemitix/thorp/core/KeyGenerator.scala

@@ -1,17 +1,19 @@
 package net.kemitix.thorp.core
 
-import java.io.File
+import java.nio.file.Path
 
-import net.kemitix.thorp.domain.RemoteKey
+import net.kemitix.thorp.domain.{RemoteKey, Sources}
 
 object KeyGenerator {
 
-  def generateKey(source: File, prefix: RemoteKey)
+  def generateKey(sources: Sources,
-                 (file: File): RemoteKey = {
+                  prefix: RemoteKey)
-    val otherPath = file.toPath.toAbsolutePath
+                 (path: Path): RemoteKey = {
-    val sourcePath = source.toPath
+    val source = sources.forPath(path)
-    val relativePath = sourcePath.relativize(otherPath)
+    val relativePath = source.relativize(path.toAbsolutePath)
-    RemoteKey(s"${prefix.key}/$relativePath")
+    RemoteKey(List(prefix.key, relativePath.toString)
+        .filterNot(_.isEmpty)
+        .mkString("/"))
   }
 
 }

core/src/main/scala/net/kemitix/thorp/core/LocalFileStream.scala

@@ -11,58 +11,66 @@ import net.kemitix.thorp.storage.api.HashService
 
 object LocalFileStream {
 
-  def findFiles(file: File,
+  def findFiles(source: Path,
                 hashService: HashService)
                (implicit c: Config,
                 logger: Logger): IO[LocalFiles] = {
 
-    val filters: Path => Boolean = Filter.isIncluded(c.filters)
+    val isIncluded: Path => Boolean = Filter.isIncluded(c.filters)
 
-    def loop(file: File): IO[LocalFiles] = {
+    def loop(path: Path): IO[LocalFiles] = {
 
-      def dirPaths(file: File): IO[Stream[File]] =
+      def dirPaths(path: Path): IO[Stream[Path]] =
-        IO(listFiles(file))
+        IO(listFiles(path))
           .map(fs =>
             Stream(fs: _*)
-              .filter(f => filters(f.toPath)))
+              .map(_.toPath)
+              .filter(isIncluded))
 
-      def recurseIntoSubDirectories(file: File): IO[LocalFiles] =
+      def recurseIntoSubDirectories(path: Path): IO[LocalFiles] =
-        file match {
+        path.toFile match {
-          case f if f.isDirectory => loop(file)
+          case f if f.isDirectory => loop(path)
-          case _ => localFile(hashService, file)
+          case _ => localFile(hashService, path)
         }
 
-      def recurse(fs: Stream[File]): IO[LocalFiles] =
+      def recurse(paths: Stream[Path]): IO[LocalFiles] =
-        fs.foldLeft(IO.pure(LocalFiles()))((acc, f) =>
+        paths.foldLeft(IO.pure(LocalFiles()))((acc, path) =>
-          recurseIntoSubDirectories(f)
+          recurseIntoSubDirectories(path)
             .flatMap(localFiles => acc.map(accLocalFiles => accLocalFiles ++ localFiles)))
 
       for {
-        _ <- logger.debug(s"- Entering: $file")
+        _ <- logger.debug(s"- Entering: $path")
-        fs <- dirPaths(file)
+        fs <- dirPaths(path)
         lfs <- recurse(fs)
-        _ <- logger.debug(s"- Leaving : $file")
+        _ <- logger.debug(s"- Leaving : $path")
       } yield lfs
     }
 
-    loop(file)
+    loop(source)
   }
 
   private def localFile(hashService: HashService,
-                        file: File)
+                        path: Path)
                        (implicit l: Logger, c: Config) = {
+    val file = path.toFile
+    val source = c.sources.forPath(path)
     for {
-      hash <- hashService.hashLocalObject(file)
+      hash <- hashService.hashLocalObject(path)
     } yield
       LocalFiles(
-        localFiles = Stream(domain.LocalFile(file, c.source, hash, generateKey(c.source, c.prefix)(file))),
+        localFiles = Stream(
+          domain.LocalFile(
+            file,
+            source.toFile,
+            hash,
+            generateKey(c.sources, c.prefix)(path))),
         count = 1,
         totalSizeBytes = file.length)
   }
 
   //TODO: Change this to return an Either[IllegalArgumentException, Array[File]]
-  private def listFiles(file: File) = {
+  private def listFiles(path: Path): Array[File] = {
-    Option(file.listFiles)
+    Option(path.toFile.listFiles)
-      .getOrElse(throw new IllegalArgumentException(s"Directory not found $file"))
+      .getOrElse(throw new IllegalArgumentException(s"Directory not found $path"))
   }
 }

core/src/main/scala/net/kemitix/thorp/core/MD5HashGenerator.scala

@@ -1,6 +1,7 @@
 package net.kemitix.thorp.core
 
 import java.io.{File, FileInputStream}
+import java.nio.file.Path
 import java.security.MessageDigest
 
 import cats.effect.IO
@@ -25,8 +26,8 @@ object MD5HashGenerator {
     md5.digest
   }
 
-  def md5File(file: File)(implicit logger: Logger): IO[MD5Hash] =
+  def md5File(path: Path)(implicit logger: Logger): IO[MD5Hash] =
-    md5FileChunk(file, 0, file.length)
+    md5FileChunk(path, 0, path.toFile.length)
 
   private def openFile(file: File, offset: Long) = IO {
     val stream = new FileInputStream(file)
@@ -68,16 +69,17 @@ object MD5HashGenerator {
     result.toInt
   }
 
-  def md5FileChunk(file: File,
+  def md5FileChunk(path: Path,
                    offset: Long,
                    size: Long)
                   (implicit logger: Logger): IO[MD5Hash] = {
+    val file = path.toFile
     val endOffset = Math.min(offset + size, file.length)
     for {
-      _ <- logger.debug(s"md5:reading:size ${file.length}:$file")
+      _ <- logger.debug(s"md5:reading:size ${file.length}:$path")
       digest <- readFile(file, offset, endOffset)
       hash = MD5Hash.fromDigest(digest)
-      _ <- logger.debug(s"md5:generated:${hash.hash}:$file")
+      _ <- logger.debug(s"md5:generated:${hash.hash}:$path")
     } yield hash
   }
 

core/src/main/scala/net/kemitix/thorp/core/PlanBuilder.scala

@@ -43,7 +43,7 @@ trait PlanBuilder {
                      hashService: HashService)
                     (implicit c: Config, l: Logger): EitherT[IO, List[String], SyncPlan] = {
     for {
-      _ <- EitherT.liftF(SyncLogging.logRunStart(c.bucket, c.prefix, c.source))
+      _ <- EitherT.liftF(SyncLogging.logRunStart(c.bucket, c.prefix, c.sources))
       actions <- gatherMetadata(storageService, hashService)
         .leftMap(error => List(error))
         .map(assemblePlan)
@@ -61,7 +61,7 @@ trait PlanBuilder {
 
   private def actionsForLocalFiles(localData: LocalFiles, remoteData: S3ObjectsData)
                                   (implicit c: Config) =
-    localData.localFiles.foldLeft(Stream[Action]())((acc, lf) => createActionFromLocalFile(lf, remoteData) ++ acc)
+    localData.localFiles.foldLeft(Stream[Action]())((acc, lf) => createActionFromLocalFile(lf, remoteData, acc) ++ acc)
 
   private def actionsForRemoteKeys(remoteData: S3ObjectsData)
                                   (implicit c: Config) =
@@ -75,16 +75,33 @@ trait PlanBuilder {
                             (implicit config: Config, l: Logger) =
     for {
       _ <- SyncLogging.logFileScan
-      localFiles <- LocalFileStream.findFiles(config.source, hashService)
+      localFiles <- findFiles(hashService)
     } yield localFiles
 
-  private def createActionFromLocalFile(lf: LocalFile, remoteData: S3ObjectsData)
+  private def findFiles(hashService: HashService)
+                       (implicit c: Config, l: Logger): IO[LocalFiles] = {
+    val ioListLocalFiles = (for {
+      source <- c.sources.paths
+    } yield LocalFileStream.findFiles(source, hashService)).sequence
+    for {
+      listLocalFiles <- ioListLocalFiles
+      localFiles = listLocalFiles.foldRight(LocalFiles()){
+        (acc, moreLocalFiles) => {
+          acc ++ moreLocalFiles
+        }
+      }
+    } yield localFiles
+  }
+
+  private def createActionFromLocalFile(lf: LocalFile,
+                                        remoteData: S3ObjectsData,
+                                        previousActions: Stream[Action])
                                        (implicit c: Config) =
-    ActionGenerator.createActions(S3MetaDataEnricher.getMetadata(lf, remoteData))
+    ActionGenerator.createActions(S3MetaDataEnricher.getMetadata(lf, remoteData), previousActions)
 
   private def createActionFromRemoteKey(rk: RemoteKey)
                                        (implicit c: Config) =
-    if (rk.isMissingLocally(c.source, c.prefix)) Action.ToDelete(c.bucket, rk, 0L)
+    if (rk.isMissingLocally(c.sources, c.prefix)) Action.ToDelete(c.bucket, rk, 0L)
     else DoNothing(c.bucket, rk, 0L)
 
 }

core/src/main/scala/net/kemitix/thorp/core/SimpleHashService.scala

@@ -0,0 +1,19 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.Path
+
+import cats.effect.IO
+import net.kemitix.thorp.domain.{Logger, MD5Hash}
+import net.kemitix.thorp.storage.api.HashService
+
+case class SimpleHashService() extends HashService {
+
+  override def hashLocalObject(path: Path)
+                              (implicit l: Logger): IO[Map[String, MD5Hash]] =
+    for {
+      md5 <- MD5HashGenerator.md5File(path)
+    } yield Map(
+      "md5" -> md5
+    )
+
+}

core/src/main/scala/net/kemitix/thorp/core/SyncLogging.scala

@@ -1,7 +1,5 @@
 package net.kemitix.thorp.core
 
-import java.io.File
-
 import cats.effect.IO
 import cats.implicits._
 import net.kemitix.thorp.domain.StorageQueueEvent.{CopyQueueEvent, DeleteQueueEvent, ErrorQueueEvent, UploadQueueEvent}
@@ -11,13 +9,15 @@ trait SyncLogging {
 
   def logRunStart(bucket: Bucket,
                   prefix: RemoteKey,
-                  source: File)
+                  sources: Sources)
-                 (implicit logger: Logger): IO[Unit] =
+                 (implicit logger: Logger): IO[Unit] = {
-    logger.info(s"Bucket: ${bucket.name}, Prefix: ${prefix.key}, Source: $source, ")
+    val sourcesList = sources.paths.mkString(", ")
+    logger.info(s"Bucket: ${bucket.name}, Prefix: ${prefix.key}, Source: $sourcesList, ")
+  }
 
   def logFileScan(implicit c: Config,
                   logger: Logger): IO[Unit] =
-    logger.info(s"Scanning local files: ${c.source}...")
+    logger.info(s"Scanning local files: ${c.sources}...")
 
   def logErrors(actions: Stream[StorageQueueEvent])
                (implicit logger: Logger): IO[Unit] =

core/src/test/scala/net/kemitix/thorp/core/ActionGeneratorSuite.scala

@@ -10,19 +10,22 @@ class ActionGeneratorSuite
   extends FunSpec {
 
   private val source = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
   private val bucket = Bucket("bucket")
-  implicit private val config: Config = Config(bucket, prefix, source = source)
+  implicit private val config: Config = Config(bucket, prefix, sources = Sources(List(sourcePath)))
-  private val fileToKey = KeyGenerator.generateKey(config.source, config.prefix) _
+  private val fileToKey = KeyGenerator.generateKey(config.sources, config.prefix) _
   val lastModified = LastModified(Instant.now())
 
     describe("create actions") {
 
-      def invoke(input: S3MetaData) = ActionGenerator.createActions(input).toList
+      val previousActions = Stream.empty[Action]
+
+      def invoke(input: S3MetaData) = ActionGenerator.createActions(input, previousActions).toList
 
       describe("#1 local exists, remote exists, remote matches - do nothing") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteMetadata = RemoteMetaData(theFile.remoteKey, theHash, lastModified)
         val input = S3MetaData(theFile, // local exists
           matchByHash = Set(theRemoteMetadata), // remote matches
@@ -36,7 +39,7 @@ class ActionGeneratorSuite
       }
       describe("#2 local exists, remote is missing, other matches - copy") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey = theFile.remoteKey
         val otherRemoteKey = prefix.resolve("other-key")
         val otherRemoteMetadata = RemoteMetaData(otherRemoteKey, theHash, lastModified)
@@ -51,7 +54,7 @@ class ActionGeneratorSuite
       }
       describe("#3 local exists, remote is missing, other no matches - upload") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val input = S3MetaData(theFile, // local exists
           matchByHash = Set.empty, // other no matches
           matchByKey = None) // remote is missing
@@ -63,7 +66,7 @@ class ActionGeneratorSuite
       }
       describe("#4 local exists, remote exists, remote no match, other matches - copy") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey = theFile.remoteKey
         val oldHash = MD5Hash("old-hash")
         val otherRemoteKey = prefix.resolve("other-key")
@@ -82,7 +85,7 @@ class ActionGeneratorSuite
       }
       describe("#5 local exists, remote exists, remote no match, other no matches - upload") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey = theFile.remoteKey
         val oldHash = MD5Hash("old-hash")
         val theRemoteMetadata = RemoteMetaData(theRemoteKey, oldHash, lastModified)

core/src/test/scala/net/kemitix/thorp/core/ConfigOptionTest.scala

@@ -0,0 +1,31 @@
+package net.kemitix.thorp.core
+
+import net.kemitix.thorp.domain.Sources
+import org.scalatest.FunSpec
+
+class ConfigOptionTest extends FunSpec with TemporaryFolder {
+
+  describe("when more than one source") {
+    it("should preserve their order") {
+      withDirectory(path1 => {
+        withDirectory(path2 => {
+          val configOptions = ConfigOptions(List(
+            ConfigOption.Source(path1),
+            ConfigOption.Source(path2),
+            ConfigOption.Bucket("bucket"),
+            ConfigOption.IgnoreGlobalOptions,
+            ConfigOption.IgnoreUserOptions
+          ))
+          val expected = Sources(List(path1, path2))
+          val result = invoke(configOptions)
+          assert(result.isRight, result)
+          assertResult(expected)(ConfigQuery.sources(configOptions))
+        })
+      })
+    }
+  }
+
+  private def invoke(configOptions: ConfigOptions) = {
+    ConfigurationBuilder.buildConfig(configOptions).unsafeRunSync
+  }
+}

core/src/test/scala/net/kemitix/thorp/core/ConfigurationBuilderTest.scala

@@ -0,0 +1,129 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.{Path, Paths}
+
+import net.kemitix.thorp.domain._
+import org.scalatest.FunSpec
+
+class ConfigurationBuilderTest extends FunSpec with TemporaryFolder {
+
+  private val pwd: Path = Paths.get(System.getenv("PWD"))
+  private val aBucket = Bucket("aBucket")
+  private val coBucket: ConfigOption.Bucket = ConfigOption.Bucket(aBucket.name)
+  private val thorpConfigFileName = ".thorp.config"
+
+  private def configOptions(options: ConfigOption*): ConfigOptions =
+    ConfigOptions(List(
+        ConfigOption.IgnoreUserOptions,
+        ConfigOption.IgnoreGlobalOptions
+      ) ++ options)
+
+  describe("when no source") {
+    it("should use the current (PWD) directory") {
+      val expected = Right(Config(aBucket, sources = Sources(List(pwd))))
+      val options = configOptions(coBucket)
+      val result = invoke(options)
+      assertResult(expected)(result)
+    }
+  }
+  describe("when has a single source with no .thorp.config") {
+    it("should only include the source once") {
+      withDirectory(aSource => {
+        val expected = Right(Sources(List(aSource)))
+        val options = configOptions(ConfigOption.Source(aSource), coBucket)
+        val result = invoke(options).map(_.sources)
+        assertResult(expected)(result)
+      })
+    }
+  }
+  describe("when has two sources") {
+    it("should include both sources in order") {
+      withDirectory(currentSource => {
+        withDirectory(previousSource => {
+          val expected = Right(List(currentSource, previousSource))
+          val options = configOptions(
+            ConfigOption.Source(currentSource),
+            ConfigOption.Source(previousSource),
+            coBucket)
+          val result = invoke(options).map(_.sources.paths)
+          assertResult(expected)(result)
+        })
+      })
+    }
+  }
+  describe("when current source has .thorp.config with source to another") {
+    it("should include both sources in order") {
+      withDirectory(currentSource => {
+        withDirectory(previousSource => {
+          writeFile(currentSource, thorpConfigFileName,
+            s"source = $previousSource")
+          val expected = Right(List(currentSource, previousSource))
+          val options = configOptions(
+            ConfigOption.Source(currentSource),
+            coBucket)
+          val result = invoke(options).map(_.sources.paths)
+          assertResult(expected)(result)
+        })
+      })
+    }
+    describe("when settings are in current and previous") {
+      it("should include some settings from both sources and some from only current") {
+        withDirectory(previousSource => {
+          withDirectory(currentSource => {
+            writeFile(currentSource, thorpConfigFileName,
+              s"source = $previousSource",
+              "bucket = current-bucket",
+              "prefix = current-prefix",
+              "include = current-include",
+              "exclude = current-exclude")
+            writeFile(previousSource, thorpConfigFileName,
+              "bucket = previous-bucket",
+              "prefix = previous-prefix",
+              "include = previous-include",
+              "exclude = previous-exclude")
+            // should have both sources in order
+            val expectedSources = Right(Sources(List(currentSource, previousSource)))
+            // should have bucket from current only
+            val expectedBuckets = Right(Bucket("current-bucket"))
+            // should have prefix from current only
+            val expectedPrefixes = Right(RemoteKey("current-prefix"))
+            // should have filters from both sources
+            val expectedFilters = Right(List(
+              Filter.Exclude("previous-exclude"),
+              Filter.Include("previous-include"),
+              Filter.Exclude("current-exclude"),
+              Filter.Include("current-include")))
+            val options = configOptions(ConfigOption.Source(currentSource))
+            val result = invoke(options)
+            assertResult(expectedSources)(result.map(_.sources))
+            assertResult(expectedBuckets)(result.map(_.bucket))
+            assertResult(expectedPrefixes)(result.map(_.prefix))
+            assertResult(expectedFilters)(result.map(_.filters))
+          })
+        })
+      }
+    }
+  }
+
+  describe("when source has thorp.config source to another source that does the same") {
+    it("should include all three sources") {
+      withDirectory(currentSource => {
+        withDirectory(parentSource => {
+          writeFile(currentSource, thorpConfigFileName, s"source = $parentSource")
+          withDirectory(grandParentSource => {
+            writeFile(parentSource, thorpConfigFileName, s"source = $grandParentSource")
+            val expected = Right(List(currentSource, parentSource, grandParentSource))
+            val options = configOptions(
+              ConfigOption.Source(currentSource),
+              coBucket)
+            val result = invoke(options).map(_.sources.paths)
+            assertResult(expected)(result)
+          })
+        })
+      })
+    }
+  }
+
+  private def invoke(configOptions: ConfigOptions) =
+    ConfigurationBuilder.buildConfig(configOptions).unsafeRunSync
+}

core/src/test/scala/net/kemitix/thorp/core/DummyHashService.scala

@@ -1,11 +1,16 @@
 package net.kemitix.thorp.core
 
-import java.io.File
+import java.nio.file.Path
 
 import cats.effect.IO
 import net.kemitix.thorp.domain.{Logger, MD5Hash}
 import net.kemitix.thorp.storage.api.HashService
 
-case class DummyHashService(hashes: Map[File, Map[String, MD5Hash]]) extends HashService {
+case class DummyHashService(hashes: Map[Path, Map[String, MD5Hash]])
-  override def hashLocalObject(file: File)(implicit l: Logger): IO[Map[String, MD5Hash]] = IO.pure(hashes(file))
+  extends HashService {
+
+  override def hashLocalObject(path: Path)
+                              (implicit l: Logger): IO[Map[String, MD5Hash]] =
+    IO.pure(hashes(path))
+
 }

core/src/test/scala/net/kemitix/thorp/core/DummyStorageService.scala

@@ -0,0 +1,41 @@
+package net.kemitix.thorp.core
+
+import java.io.File
+
+import cats.data.EitherT
+import cats.effect.IO
+import net.kemitix.thorp.domain._
+import net.kemitix.thorp.storage.api.StorageService
+
+case class DummyStorageService(s3ObjectData: S3ObjectsData,
+                               uploadFiles: Map[File, (RemoteKey, MD5Hash)])
+  extends StorageService {
+
+  override def shutdown: IO[StorageQueueEvent] =
+    IO.pure(StorageQueueEvent.ShutdownQueueEvent())
+
+  override def listObjects(bucket: Bucket,
+                           prefix: RemoteKey)
+                          (implicit l: Logger): EitherT[IO, String, S3ObjectsData] =
+    EitherT.liftF(IO.pure(s3ObjectData))
+
+  override def upload(localFile: LocalFile,
+                      bucket: Bucket,
+                      batchMode: Boolean,
+                      uploadEventListener: UploadEventListener,
+                      tryCount: Int): IO[StorageQueueEvent] = {
+    val (remoteKey, md5Hash) = uploadFiles(localFile.file)
+    IO.pure(StorageQueueEvent.UploadQueueEvent(remoteKey, md5Hash))
+  }
+
+  override def copy(bucket: Bucket,
+                    sourceKey: RemoteKey,
+                    hash: MD5Hash,
+                    targetKey: RemoteKey): IO[StorageQueueEvent] =
+    IO.pure(StorageQueueEvent.CopyQueueEvent(targetKey))
+
+  override def delete(bucket: Bucket,
+                      remoteKey: RemoteKey): IO[StorageQueueEvent] =
+    IO.pure(StorageQueueEvent.DeleteQueueEvent(remoteKey))
+
+}

core/src/test/scala/net/kemitix/thorp/core/KeyGeneratorSuite.scala

@@ -2,32 +2,30 @@ package net.kemitix.thorp.core
 
 import java.io.File
 
-import net.kemitix.thorp.domain.{Bucket, Config, RemoteKey}
+import net.kemitix.thorp.domain.{Bucket, Config, RemoteKey, Sources}
 import org.scalatest.FunSpec
 
 class KeyGeneratorSuite extends FunSpec {
 
   private val source: File = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
-    implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
+  implicit private val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
-    private val fileToKey = KeyGenerator.generateKey(config.source, config.prefix) _
+  private val fileToKey = KeyGenerator.generateKey(config.sources, config.prefix) _
 
   describe("key generator") {
-      def resolve(subdir: String): File = {
-        source.toPath.resolve(subdir).toFile
-      }
 
     describe("when file is within source") {
       it("has a valid key") {
         val subdir = "subdir"
-          assertResult(RemoteKey(s"${prefix.key}/$subdir"))(fileToKey(resolve(subdir)))
+        assertResult(RemoteKey(s"${prefix.key}/$subdir"))(fileToKey(sourcePath.resolve(subdir)))
       }
     }
 
     describe("when file is deeper within source") {
       it("has a valid key") {
         val subdir = "subdir/deeper/still"
-          assertResult(RemoteKey(s"${prefix.key}/$subdir"))(fileToKey(resolve(subdir)))
+        assertResult(RemoteKey(s"${prefix.key}/$subdir"))(fileToKey(sourcePath.resolve(subdir)))
       }
     }
   }

core/src/test/scala/net/kemitix/thorp/core/LocalFileStreamSuite.scala

@@ -2,22 +2,23 @@ package net.kemitix.thorp.core
 
 import java.nio.file.Paths
 
-import net.kemitix.thorp.domain.{Config, LocalFile, Logger, MD5HashData}
+import net.kemitix.thorp.domain.{Config, LocalFile, Logger, MD5HashData, Sources}
 import net.kemitix.thorp.storage.api.HashService
 import org.scalatest.FunSpec
 
 class LocalFileStreamSuite extends FunSpec {
 
-  private val uploadResource = Resource(this, "upload")
+  private val source = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val hashService: HashService = DummyHashService(Map(
     file("root-file") -> Map("md5" -> MD5HashData.Root.hash),
     file("subdir/leaf-file") -> Map("md5" -> MD5HashData.Leaf.hash)
   ))
 
   private def file(filename: String) =
-    uploadResource.toPath.resolve(Paths.get(filename)).toFile
+    sourcePath.resolve(Paths.get(filename))
 
-  implicit private val config: Config = Config(source = uploadResource)
+  implicit private val config: Config = Config(sources = Sources(List(sourcePath)))
   implicit private val logger: Logger = new DummyLogger
 
   describe("findFiles") {
@@ -37,7 +38,7 @@ class LocalFileStreamSuite extends FunSpec {
     }
   }
 
-  private def invoke = {
+  private def invoke =
-    LocalFileStream.findFiles(uploadResource, hashService).unsafeRunSync
+    LocalFileStream.findFiles(sourcePath, hashService).unsafeRunSync
-  }
+
 }

core/src/test/scala/net/kemitix/thorp/core/MD5HashGeneratorTest.scala

@@ -7,37 +7,38 @@ import org.scalatest.FunSpec
 class MD5HashGeneratorTest extends FunSpec {
 
   private val source = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
-  implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
+  implicit private val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
   implicit private val logger: Logger = new DummyLogger
 
   describe("read a small file (smaller than buffer)") {
-    val file = Resource(this, "upload/root-file")
+    val path = Resource(this, "upload/root-file").toPath
     it("should generate the correct hash") {
-      val result = MD5HashGenerator.md5File(file).unsafeRunSync
+      val result = MD5HashGenerator.md5File(path).unsafeRunSync
       assertResult(Root.hash)(result)
     }
   }
   describe("read a large file (bigger than buffer)") {
-    val file = Resource(this, "big-file")
+    val path = Resource(this, "big-file").toPath
     it("should generate the correct hash") {
       val expected = MD5HashData.BigFile.hash
-      val result = MD5HashGenerator.md5File(file).unsafeRunSync
+      val result = MD5HashGenerator.md5File(path).unsafeRunSync
       assertResult(expected)(result)
     }
   }
   describe("read chunks of file") {
-    val file = Resource(this, "big-file")
+    val path = Resource(this, "big-file").toPath
     it("should generate the correct hash for first chunk of the file") {
       val part1 = MD5HashData.BigFile.Part1
       val expected = part1.hash
-      val result = MD5HashGenerator.md5FileChunk(file, part1.offset, part1.size).unsafeRunSync
+      val result = MD5HashGenerator.md5FileChunk(path, part1.offset, part1.size).unsafeRunSync
       assertResult(expected)(result)
     }
     it("should generate the correcy hash for second chunk of the file") {
       val part2 = MD5HashData.BigFile.Part2
       val expected = part2.hash
-      val result = MD5HashGenerator.md5FileChunk(file, part2.offset, part2.size).unsafeRunSync
+      val result = MD5HashGenerator.md5FileChunk(path, part2.offset, part2.size).unsafeRunSync
       assertResult(expected)(result)
     }
   }

core/src/test/scala/net/kemitix/thorp/core/PlanBuilderTest.scala

@@ -0,0 +1,404 @@
+package net.kemitix.thorp.core
+
+import java.io.File
+import java.nio.file.Path
+
+import net.kemitix.thorp.core.Action.{DoNothing, ToCopy, ToDelete, ToUpload}
+import net.kemitix.thorp.domain._
+import net.kemitix.thorp.storage.api.{HashService, StorageService}
+import org.scalatest.FreeSpec
+
+class PlanBuilderTest extends FreeSpec with TemporaryFolder {
+
+  private val planBuilder = new PlanBuilder {}
+  private val emptyS3ObjectData = S3ObjectsData()
+  private implicit val logger: Logger = new DummyLogger
+
+  val lastModified: LastModified = LastModified()
+
+  "create a plan" - {
+
+    val hashService = SimpleHashService()
+
+    "one source" - {
+      "a file" - {
+        val filename = "aFile"
+        val remoteKey = RemoteKey(filename)
+        "with no matching remote key" - {
+          "with no other remote key with matching hash" - {
+            "upload file" in {
+              withDirectory(source => {
+                val file = createFile(source, filename, "file-content")
+                val hash = md5Hash(file)
+
+                val expected = Right(List(
+                  toUpload(remoteKey, hash, source, file)
+                ))
+
+                val storageService = DummyStorageService(emptyS3ObjectData, Map(
+                  file -> (remoteKey, hash)
+                ))
+
+                val result = invoke(storageService, hashService, configOptions(
+                  ConfigOption.Source(source),
+                  ConfigOption.Bucket("a-bucket")))
+
+                assertResult(expected)(result)
+              })
+            }
+          }
+          "with another remote key with matching hash" - {
+            "copy file" in {
+              withDirectory(source => {
+                val anOtherFilename = "other"
+                val content = "file-content"
+                val aFile = createFile(source, filename, content)
+                val anOtherFile = createFile(source, anOtherFilename, content)
+                val aHash = md5Hash(aFile)
+
+                val anOtherKey = RemoteKey("other")
+
+                val expected = Right(List(
+                  toCopy(anOtherKey, aHash, remoteKey)
+                ))
+
+                val s3ObjectsData = S3ObjectsData(
+                  byHash = Map(aHash -> Set(KeyModified(anOtherKey, lastModified))),
+                  byKey = Map(anOtherKey -> HashModified(aHash, lastModified))
+                )
+
+                val storageService = DummyStorageService(s3ObjectsData, Map(
+                  aFile -> (remoteKey, aHash)
+                ))
+
+                val result = invoke(storageService, hashService, configOptions(
+                  ConfigOption.Source(source),
+                  ConfigOption.Bucket("a-bucket")))
+
+                assertResult(expected)(result)
+              })
+            }
+          }
+        }
+        "with matching remote key" - {
+          "with matching hash" - {
+            "do nothing" in {
+              withDirectory(source => {
+                val file = createFile(source, filename, "file-content")
+                val hash = md5Hash(file)
+
+                // DoNothing actions should have been filtered out of the plan
+                val expected = Right(List())
+
+                val s3ObjectsData = S3ObjectsData(
+                  byHash = Map(hash -> Set(KeyModified(remoteKey, lastModified))),
+                  byKey = Map(remoteKey -> HashModified(hash, lastModified))
+                )
+
+                val storageService = DummyStorageService(s3ObjectsData, Map(
+                  file -> (remoteKey, hash)
+                ))
+
+                val result = invoke(storageService, hashService, configOptions(
+                  ConfigOption.Source(source),
+                  ConfigOption.Bucket("a-bucket")))
+
+                assertResult(expected)(result)
+              })
+            }
+          }
+          "with different hash" - {
+            "with no matching remote hash" - {
+              "upload file" in {
+                withDirectory(source => {
+                  val file = createFile(source, filename, "file-content")
+                  val currentHash = md5Hash(file)
+                  val originalHash = MD5Hash("original-file-content")
+
+                  val expected = Right(List(
+                    toUpload(remoteKey, currentHash, source, file)
+                  ))
+
+                  val s3ObjectsData = S3ObjectsData(
+                    byHash = Map(originalHash -> Set(KeyModified(remoteKey, lastModified))),
+                    byKey = Map(remoteKey -> HashModified(originalHash, lastModified))
+                  )
+
+                  val storageService = DummyStorageService(s3ObjectsData, Map(
+                    file -> (remoteKey, currentHash)
+                  ))
+
+                  val result = invoke(storageService, hashService, configOptions(
+                    ConfigOption.Source(source),
+                    ConfigOption.Bucket("a-bucket")))
+
+                  assertResult(expected)(result)
+                })
+              }
+            }
+            "with matching remote hash" - {
+              "copy file" in {
+                withDirectory(source => {
+                  val file = createFile(source, filename, "file-content")
+                  val hash = md5Hash(file)
+                  val sourceKey = RemoteKey("other-key")
+
+                  val expected = Right(List(
+                    toCopy(sourceKey, hash, remoteKey)
+                  ))
+
+                  val s3ObjectsData = S3ObjectsData(
+                    byHash = Map(hash -> Set(KeyModified(sourceKey, lastModified))),
+                    byKey = Map()
+                  )
+
+                  val storageService = DummyStorageService(s3ObjectsData, Map(
+                    file -> (remoteKey, hash)
+                  ))
+
+                  val result = invoke(storageService, hashService, configOptions(
+                    ConfigOption.Source(source),
+                    ConfigOption.Bucket("a-bucket")))
+
+                  assertResult(expected)(result)
+                })
+              }
+            }
+          }
+        }
+      }
+      "a remote key" - {
+        val filename = "aFile"
+        val remoteKey = RemoteKey(filename)
+        "with a matching local file" - {
+          "do nothing" in {
+            withDirectory(source => {
+              val file = createFile(source, filename, "file-content")
+              val hash = md5Hash(file)
+
+              // DoNothing actions should have been filtered out of the plan
+              val expected = Right(List())
+
+              val s3ObjectsData = S3ObjectsData(
+                byHash = Map(hash -> Set(KeyModified(remoteKey, lastModified))),
+                byKey = Map(remoteKey -> HashModified(hash, lastModified))
+              )
+
+              val storageService = DummyStorageService(s3ObjectsData, Map(
+                file -> (remoteKey, hash)
+              ))
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(source),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          }
+        }
+        "with no matching local file" - {
+          "delete remote key" ignore {
+            withDirectory(source => {
+              val hash = MD5Hash("file-content")
+
+              val expected = Right(List(
+                toDelete(remoteKey)
+              ))
+
+              val s3ObjectsData = S3ObjectsData(
+                byHash = Map(hash -> Set(KeyModified(remoteKey, lastModified))),
+                byKey = Map(remoteKey -> HashModified(hash, lastModified))
+              )
+
+              val storageService = DummyStorageService(s3ObjectsData, Map.empty)
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(source),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          }
+        }
+      }
+    }
+
+    "two sources" - {
+      val filename1 = "file-1"
+      val filename2 = "file-2"
+      val remoteKey1 = RemoteKey(filename1)
+      val remoteKey2 = RemoteKey(filename2)
+      "unique files in both" - {
+        "upload all files" in {
+          withDirectory(firstSource => {
+            val fileInFirstSource = createFile(firstSource, filename1, "file-1-content")
+            val hash1 = md5Hash(fileInFirstSource)
+
+            withDirectory(secondSource => {
+              val fileInSecondSource = createFile(secondSource, filename2, "file-2-content")
+              val hash2 = md5Hash(fileInSecondSource)
+
+              val expected = Right(List(
+                toUpload(remoteKey2, hash2, secondSource, fileInSecondSource),
+                toUpload(remoteKey1, hash1, firstSource, fileInFirstSource)
+              ))
+
+              val storageService = DummyStorageService(emptyS3ObjectData, Map(
+                fileInFirstSource -> (remoteKey1, hash1),
+                fileInSecondSource -> (remoteKey2, hash2)))
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(firstSource),
+                ConfigOption.Source(secondSource),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          })
+        }
+      }
+      "same filename in both" - {
+        "only upload file in first source" in {
+          withDirectory(firstSource => {
+            val fileInFirstSource: File = createFile(firstSource, filename1, "file-1-content")
+            val hash1 = md5Hash(fileInFirstSource)
+
+            withDirectory(secondSource => {
+              val fileInSecondSource: File = createFile(secondSource, filename1, "file-2-content")
+              val hash2 = md5Hash(fileInSecondSource)
+
+              val expected = Right(List(
+                toUpload(remoteKey1, hash1, firstSource, fileInFirstSource)
+              ))
+
+              val storageService = DummyStorageService(emptyS3ObjectData, Map(
+                fileInFirstSource -> (remoteKey1, hash1),
+                fileInSecondSource -> (remoteKey2, hash2)))
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(firstSource),
+                ConfigOption.Source(secondSource),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          })
+        }
+      }
+      "with a remote file only present in second source" -  {
+        "do not delete it " in {
+          withDirectory(firstSource => {
+
+            withDirectory(secondSource => {
+              val fileInSecondSource = createFile(secondSource, filename2, "file-2-content")
+              val hash2 = md5Hash(fileInSecondSource)
+
+              val expected = Right(List())
+
+              val s3ObjectData = S3ObjectsData(
+                byHash = Map(hash2 -> Set(KeyModified(remoteKey2, lastModified))),
+                byKey = Map(remoteKey2 -> HashModified(hash2, lastModified)))
+
+              val storageService = DummyStorageService(s3ObjectData, Map(
+                fileInSecondSource -> (remoteKey2, hash2)))
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(firstSource),
+                ConfigOption.Source(secondSource),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          })
+        }
+      }
+      "with remote file only present in first source" - {
+        "do not delete it" in {
+          withDirectory(firstSource => {
+            val fileInFirstSource: File = createFile(firstSource, filename1, "file-1-content")
+            val hash1 = md5Hash(fileInFirstSource)
+
+            withDirectory(secondSource => {
+
+              val expected = Right(List())
+
+              val s3ObjectData = S3ObjectsData(
+                byHash = Map(hash1 -> Set(KeyModified(remoteKey1, lastModified))),
+                byKey = Map(remoteKey1 -> HashModified(hash1, lastModified)))
+
+              val storageService = DummyStorageService(s3ObjectData, Map(
+                fileInFirstSource -> (remoteKey1, hash1)))
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(firstSource),
+                ConfigOption.Source(secondSource),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          })
+        }
+      }
+      "with remote file not present in either source" - {
+        "delete from remote" in {
+          withDirectory(firstSource => {
+
+            withDirectory(secondSource => {
+
+              val expected = Right(List(
+                toDelete(remoteKey1)
+              ))
+
+              val s3ObjectData = S3ObjectsData(
+                byKey = Map(remoteKey1 -> HashModified(MD5Hash(""), lastModified)))
+
+              val storageService = DummyStorageService(s3ObjectData, Map())
+
+              val result = invoke(storageService, hashService, configOptions(
+                ConfigOption.Source(firstSource),
+                ConfigOption.Source(secondSource),
+                ConfigOption.Bucket("a-bucket")))
+
+              assertResult(expected)(result)
+            })
+          })
+        }
+      }
+    }
+
+    def md5Hash(file: File) = {
+      hashService.hashLocalObject(file.toPath).unsafeRunSync()("md5")
+    }
+
+  }
+
+  private def toUpload(remoteKey: RemoteKey,
+                       md5Hash: MD5Hash,
+                       source: Path,
+                       file: File): (String, String, String, String, String) =
+    ("upload", remoteKey.key, md5Hash.hash, source.toString, file.toString)
+
+  private def toCopy(sourceKey: RemoteKey,
+                     md5Hash: MD5Hash,
+                     targetKey: RemoteKey): (String, String, String, String, String) =
+    ("copy", sourceKey.key, md5Hash.hash, targetKey.key, "")
+
+  private def toDelete(remoteKey: RemoteKey): (String, String, String, String, String) =
+    ("delete", remoteKey.key, "", "", "")
+
+  private def configOptions(configOptions: ConfigOption*): ConfigOptions =
+    ConfigOptions(List(configOptions:_*))
+
+  private def invoke(storageService: StorageService,
+                     hashService: HashService,
+                     configOptions: ConfigOptions): Either[List[String], List[(String, String, String, String, String)]] =
+    planBuilder.createPlan(storageService, hashService, configOptions)
+      .value.unsafeRunSync().map(_.actions.toList.map({
+      case ToUpload(_, lf, _) => ("upload", lf.remoteKey.key, lf.hashes("md5").hash, lf.source.toString, lf.file.toString)
+      case ToDelete(_, remoteKey, _) => ("delete", remoteKey.key, "", "", "")
+      case ToCopy(_, sourceKey, hash, targetKey, _) => ("copy", sourceKey.key, hash.hash, targetKey.key, "")
+      case DoNothing(_, remoteKey, _) => ("do-nothing", remoteKey.key, "", "", "")
+      case x => ("other", x.toString, "", "", "")
+    }))
+
+}

core/src/test/scala/net/kemitix/thorp/core/S3MetaDataEnricherSuite.scala

@@ -10,9 +10,10 @@ class S3MetaDataEnricherSuite
   extends FunSpec {
 
   private val source = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
-  implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
+  implicit private val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
-  private val fileToKey = KeyGenerator.generateKey(config.source, config.prefix) _
+  private val fileToKey = KeyGenerator.generateKey(config.sources, config.prefix) _
   val lastModified = LastModified(Instant.now())
 
   def getMatchesByKey(status: (Option[HashModified], Set[(MD5Hash, KeyModified)])): Option[HashModified] = {
@@ -29,7 +30,7 @@ class S3MetaDataEnricherSuite
 
       describe("#1a local exists, remote exists, remote matches, other matches - do nothing") {
         val theHash: MD5Hash = MD5Hash("the-file-hash")
-        val theFile: LocalFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile: LocalFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey: RemoteKey = theFile.remoteKey
         val s3: S3ObjectsData = S3ObjectsData(
           byHash = Map(theHash -> Set(KeyModified(theRemoteKey, lastModified))),
@@ -46,7 +47,7 @@ class S3MetaDataEnricherSuite
       }
       describe("#1b local exists, remote exists, remote matches, other no matches - do nothing") {
         val theHash: MD5Hash = MD5Hash("the-file-hash")
-        val theFile: LocalFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile: LocalFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey: RemoteKey = prefix.resolve("the-file")
         val s3: S3ObjectsData = S3ObjectsData(
           byHash = Map(theHash -> Set(KeyModified(theRemoteKey, lastModified))),
@@ -63,7 +64,7 @@ class S3MetaDataEnricherSuite
       }
       describe("#2 local exists, remote is missing, remote no match, other matches - copy") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val otherRemoteKey = RemoteKey("other-key")
         val s3: S3ObjectsData = S3ObjectsData(
           byHash = Map(theHash -> Set(KeyModified(otherRemoteKey, lastModified))),
@@ -80,11 +81,8 @@ class S3MetaDataEnricherSuite
       }
       describe("#3 local exists, remote is missing, remote no match, other no matches - upload") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
-        val s3: S3ObjectsData = S3ObjectsData(
+        val s3: S3ObjectsData = S3ObjectsData()
-          byHash = Map(),
-          byKey = Map()
-        )
         it("generates valid metadata") {
           val expected = S3MetaData(theFile,
             matchByHash = Set.empty,
@@ -95,7 +93,7 @@ class S3MetaDataEnricherSuite
       }
       describe("#4 local exists, remote exists, remote no match, other matches - copy") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey = theFile.remoteKey
         val oldHash = MD5Hash("old-hash")
         val otherRemoteKey = prefix.resolve("other-key")
@@ -120,7 +118,7 @@ class S3MetaDataEnricherSuite
       }
       describe("#5 local exists, remote exists, remote no match, other no matches - upload") {
         val theHash = MD5Hash("the-hash")
-        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), source, fileToKey)
+        val theFile = LocalFile.resolve("the-file", md5HashMap(theHash), sourcePath, fileToKey)
         val theRemoteKey = theFile.remoteKey
         val oldHash = MD5Hash("old-hash")
         val s3: S3ObjectsData = S3ObjectsData(
@@ -148,11 +146,11 @@ class S3MetaDataEnricherSuite
 
   describe("getS3Status") {
     val hash = MD5Hash("hash")
-    val localFile = LocalFile.resolve("the-file", md5HashMap(hash), source, fileToKey)
+    val localFile = LocalFile.resolve("the-file", md5HashMap(hash), sourcePath, fileToKey)
     val key = localFile.remoteKey
-    val keyOtherKey = LocalFile.resolve("other-key-same-hash", md5HashMap(hash), source, fileToKey)
+    val keyOtherKey = LocalFile.resolve("other-key-same-hash", md5HashMap(hash), sourcePath, fileToKey)
     val diffHash = MD5Hash("diff")
-    val keyDiffHash = LocalFile.resolve("other-key-diff-hash", md5HashMap(diffHash), source, fileToKey)
+    val keyDiffHash = LocalFile.resolve("other-key-diff-hash", md5HashMap(diffHash), sourcePath, fileToKey)
     val lastModified = LastModified(Instant.now)
     val s3ObjectsData: S3ObjectsData = S3ObjectsData(
       byHash = Map(
@@ -175,7 +173,7 @@ class S3MetaDataEnricherSuite
     }
 
     describe("when remote key does not exist and no others matches hash") {
-      val localFile = LocalFile.resolve("missing-file", md5HashMap(MD5Hash("unique")), source, fileToKey)
+      val localFile = LocalFile.resolve("missing-file", md5HashMap(MD5Hash("unique")), sourcePath, fileToKey)
       it("should return no matches by key") {
         val result = getMatchesByKey(invoke(localFile))
         assert(result.isEmpty)

core/src/test/scala/net/kemitix/thorp/core/SyncSuite.scala

@@ -17,9 +17,11 @@ class SyncSuite
   extends FunSpec {
 
   private val source = Resource(this, "upload")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
-  private val configOptions = ConfigOptions(List(
+  private val configOptions =
-    ConfigOption.Source(source.toPath),
+    ConfigOptions(List(
+      ConfigOption.Source(sourcePath),
       ConfigOption.Bucket("bucket"),
       ConfigOption.Prefix("prefix"),
       ConfigOption.IgnoreGlobalOptions,
@@ -35,19 +37,23 @@ class SyncSuite
   // source contains the files root-file and subdir/leaf-file
   val rootRemoteKey = RemoteKey("prefix/root-file")
   val leafRemoteKey = RemoteKey("prefix/subdir/leaf-file")
-  val rootFile: LocalFile = LocalFile.resolve("root-file", md5HashMap(Root.hash), source, _ => rootRemoteKey)
+  val rootFile: LocalFile =
+    LocalFile.resolve("root-file", md5HashMap(Root.hash), sourcePath, _ => rootRemoteKey)
+  val leafFile: LocalFile =
+    LocalFile.resolve("subdir/leaf-file", md5HashMap(Leaf.hash), sourcePath, _ => leafRemoteKey)
 
-  private def md5HashMap(md5Hash: MD5Hash): Map[String, MD5Hash] = {
+  private def md5HashMap(md5Hash: MD5Hash): Map[String, MD5Hash] =
     Map("md5" -> md5Hash)
-  }
 
-  val leafFile: LocalFile = LocalFile.resolve("subdir/leaf-file", md5HashMap(Leaf.hash), source, _ => leafRemoteKey)
+  val hashService =
-
+    DummyHashService(Map(
-  val hashService = DummyHashService(Map(
       file("root-file") -> Map("md5" -> MD5HashData.Root.hash),
       file("subdir/leaf-file") -> Map("md5" -> MD5HashData.Leaf.hash)
     ))
 
+  private def file(filename: String) =
+    sourcePath.resolve(Paths.get(filename))
+
   def invokeSubject(storageService: StorageService,
                     hashService: HashService,
                     configOptions: ConfigOptions): Either[List[String], SyncPlan] = {
@@ -62,9 +68,7 @@ class SyncSuite
   }
 
   describe("when all files should be uploaded") {
-    val storageService = new RecordingStorageService(testBucket, S3ObjectsData(
+    val storageService = new RecordingStorageService(testBucket, S3ObjectsData())
-      byHash = Map(),
-      byKey = Map()))
     it("uploads all files") {
       val expected = Right(Set(
         ToUpload(testBucket, rootFile, rootFile.file.length),
@@ -74,9 +78,6 @@ class SyncSuite
     }
   }
 
-  private def file(filename: String) =
-    source.toPath.resolve(Paths.get(filename)).toFile
-
   describe("when no files should be uploaded") {
     val s3ObjectsData = S3ObjectsData(
       byHash = Map(

core/src/test/scala/net/kemitix/thorp/core/TemporaryFolder.scala

@@ -0,0 +1,43 @@
+package net.kemitix.thorp.core
+
+import java.io.{File, IOException, PrintWriter}
+import java.nio.file.attribute.BasicFileAttributes
+import java.nio.file.{FileVisitResult, Files, Path, SimpleFileVisitor}
+
+import scala.util.Try
+
+trait TemporaryFolder {
+
+  def withDirectory(testCode: Path => Any): Any = {
+    val dir: Path = Files.createTempDirectory("thorp-temp")
+    val t = Try(testCode(dir))
+    remove(dir)
+    t.get
+  }
+
+  def remove(root: Path): Unit = {
+    Files.walkFileTree(root, new SimpleFileVisitor[Path] {
+      override def visitFile(file: Path, attrs: BasicFileAttributes): FileVisitResult = {
+        Files.delete(file)
+        FileVisitResult.CONTINUE
+      }
+      override def postVisitDirectory(dir: Path, exc: IOException): FileVisitResult = {
+        Files.delete(dir)
+        FileVisitResult.CONTINUE
+      }
+    })
+  }
+
+  def writeFile(directory: Path, name: String, contents: String*): Unit = {
+    directory.toFile.mkdirs
+    val pw = new PrintWriter(directory.resolve(name).toFile, "UTF-8")
+    contents.foreach(pw.println)
+    pw.close()
+  }
+
+  def createFile(path: Path, name: String, content: String*): File = {
+    writeFile(path, name, content:_*)
+    path.resolve(name).toFile
+  }
+
+}

domain/src/main/scala/net/kemitix/thorp/domain/Config.scala

@@ -1,10 +1,8 @@
 package net.kemitix.thorp.domain
 
-import java.io.File
-
 final case class Config(bucket: Bucket = Bucket(""),
                         prefix: RemoteKey = RemoteKey(""),
                         filters: List[Filter] = List(),
                         debug: Boolean = false,
                         batchMode: Boolean = false,
-                        source: File)
+                        sources: Sources)

domain/src/main/scala/net/kemitix/thorp/domain/LastModified.scala

@@ -2,4 +2,4 @@ package net.kemitix.thorp.domain
 
 import java.time.Instant
 
-final case class LastModified(when: Instant)
+final case class LastModified(when: Instant = Instant.now)

domain/src/main/scala/net/kemitix/thorp/domain/LocalFile.scala

@@ -21,9 +21,9 @@ final case class LocalFile(file: File, source: File, hashes: Map[String, MD5Hash
 object LocalFile {
   def resolve(path: String,
               md5Hashes: Map[String, MD5Hash],
-              source: File,
+              source: Path,
-              fileToKey: File => RemoteKey): LocalFile = {
+              pathToKey: Path => RemoteKey): LocalFile = {
-    val file = source.toPath.resolve(path).toFile
+    val resolvedPath = source.resolve(path)
-    LocalFile(file, source, md5Hashes, fileToKey(file))
+    LocalFile(resolvedPath.toFile, source.toFile, md5Hashes, pathToKey(resolvedPath))
   }
 }

domain/src/main/scala/net/kemitix/thorp/domain/RemoteKey.scala

@@ -1,24 +1,28 @@
 package net.kemitix.thorp.domain
 
 import java.io.File
-import java.nio.file.Paths
+import java.nio.file.{Path, Paths}
 
 final case class RemoteKey(key: String) {
 
-  def asFile(source: File, prefix: RemoteKey): File =
+  def asFile(source: Path, prefix: RemoteKey): Option[File] =
-    source.toPath.resolve(relativeTo(prefix)).toFile
+    if (key.length == 0) None
+    else Some(source.resolve(relativeTo(prefix)).toFile)
 
   private def relativeTo(prefix: RemoteKey) = {
     prefix match {
-      case RemoteKey("") => Paths.get(prefix.key)
+      case RemoteKey("") => Paths.get(key)
       case _ => Paths.get(prefix.key).relativize(Paths.get(key))
     }
   }
 
-  def isMissingLocally(source: File, prefix: RemoteKey): Boolean =
+  def isMissingLocally(sources: Sources, prefix: RemoteKey): Boolean =
-    ! asFile(source, prefix).exists
+    !sources.paths.exists(source => asFile(source, prefix) match {
+      case Some(file) => file.exists
+      case None => false
+    })
 
   def resolve(path: String): RemoteKey =
-    RemoteKey(key + "/" + path)
+    RemoteKey(List(key, path).filterNot(_.isEmpty).mkString("/"))
 
 }

domain/src/main/scala/net/kemitix/thorp/domain/S3ObjectsData.scala

@@ -3,5 +3,5 @@ package net.kemitix.thorp.domain
 /**
   * A list of objects and their MD5 hash values.
   */
-final case class S3ObjectsData(byHash: Map[MD5Hash, Set[KeyModified]],
+final case class S3ObjectsData(byHash: Map[MD5Hash, Set[KeyModified]] = Map.empty,
-                               byKey: Map[RemoteKey, HashModified])
+                               byKey: Map[RemoteKey, HashModified] = Map.empty)

domain/src/main/scala/net/kemitix/thorp/domain/Sources.scala

@@ -0,0 +1,26 @@
+package net.kemitix.thorp.domain
+
+import java.nio.file.Path
+
+/**
+  * The paths to synchronise with target.
+  *
+  * The first source path takes priority over those later in the list,
+  * etc. Where there is any file with the same relative path within
+  * more than one source, the file in the first listed path is
+  * uploaded, and the others are ignored.
+  */
+case class Sources(paths: List[Path]) {
+  def ++(path: Path): Sources = this ++ List(path)
+  def ++(otherPaths: List[Path]): Sources = Sources(paths ++ otherPaths)
+
+  /**
+    * Returns the source path for the given path.
+    *
+    * @param path the path to find the matching source
+    * @return the source for the path
+    * @throws NoSuchElementException if no source matches the path
+    */
+  def forPath(path: Path): Path =
+    paths.find(source => path.startsWith(source)).get
+}

domain/src/test/scala/net/kemitix/thorp/domain/RemoteKeyTest.scala

@@ -0,0 +1,72 @@
+package net.kemitix.thorp.domain
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.FreeSpec
+
+class RemoteKeyTest extends FreeSpec {
+
+  private val emptyKey = RemoteKey("")
+
+  "create a RemoteKey" - {
+    "can resolve a path" - {
+      "when key is empty" in {
+        val key = emptyKey
+        val path = "path"
+        val expected = RemoteKey("path")
+        val result = key.resolve(path)
+        assertResult(expected)(result)
+      }
+      "when path is empty" in  {
+        val key = RemoteKey("key")
+        val path = ""
+        val expected = RemoteKey("key")
+        val result = key.resolve(path)
+        assertResult(expected)(result)
+      }
+      "when key and path are empty" in {
+        val key = emptyKey
+        val path = ""
+        val expected = emptyKey
+        val result = key.resolve(path)
+        assertResult(expected)(result)
+      }
+    }
+    "asFile" - {
+      "when key and prefix are non-empty" in {
+        val key = RemoteKey("prefix/key")
+        val source = Paths.get("source")
+        val prefix = RemoteKey("prefix")
+        val expected = Some(new File("source/key"))
+        val result = key.asFile(source, prefix)
+        assertResult(expected)(result)
+      }
+      "when prefix is empty" in {
+        val key = RemoteKey("key")
+        val source = Paths.get("source")
+        val prefix = emptyKey
+        val expected = Some(new File("source/key"))
+        val result = key.asFile(source, prefix)
+        assertResult(expected)(result)
+      }
+      "when key is empty" in {
+        val key = emptyKey
+        val source = Paths.get("source")
+        val prefix = RemoteKey("prefix")
+        val expected = None
+        val result = key.asFile(source, prefix)
+        assertResult(expected)(result)
+      }
+      "when key and prefix are empty" in {
+        val key = emptyKey
+        val source = Paths.get("source")
+        val prefix = emptyKey
+        val expected = None
+        val result = key.asFile(source, prefix)
+        assertResult(expected)(result)
+      }
+    }
+  }
+
+}

storage-api/src/main/scala/net/kemitix/thorp/storage/api/HashService.scala

@@ -1,6 +1,6 @@
 package net.kemitix.thorp.storage.api
 
-import java.io.File
+import java.nio.file.Path
 
 import cats.effect.IO
 import net.kemitix.thorp.domain.{Logger, MD5Hash}
@@ -10,6 +10,7 @@ import net.kemitix.thorp.domain.{Logger, MD5Hash}
   */
 trait HashService {
 
-  def hashLocalObject(file: File)(implicit l: Logger): IO[Map[String, MD5Hash]]
+  def hashLocalObject(path: Path)
+                     (implicit l: Logger): IO[Map[String, MD5Hash]]
 
 }

storage-aws/src/main/scala/net/kemitix/thorp/storage/aws/ETagGenerator.scala

@@ -1,6 +1,6 @@
 package net.kemitix.thorp.storage.aws
 
-import java.io.File
+import java.nio.file.Path
 
 import cats.effect.IO
 import cats.implicits._
@@ -12,11 +12,11 @@ import net.kemitix.thorp.domain.{Logger, MD5Hash}
 
 trait ETagGenerator {
 
-  def eTag(file: File)(implicit l: Logger): IO[String]= {
+  def eTag(path: Path)(implicit l: Logger): IO[String]= {
-    val partSize = calculatePartSize(file)
+    val partSize = calculatePartSize(path)
-    val parts = numParts(file.length, partSize)
+    val parts = numParts(path.toFile.length, partSize)
     partsIndex(parts)
-      .map(digestChunk(file, partSize)).sequence
+      .map(digestChunk(path, partSize)).sequence
       .map(concatenateDigests)
       .map(MD5HashGenerator.hex)
       .map(hash => s"$hash-$parts")
@@ -28,8 +28,8 @@ trait ETagGenerator {
   private def concatenateDigests: List[Array[Byte]] => Array[Byte] =
     lab => lab.foldLeft(Array[Byte]())((acc, ab) => acc ++ ab)
 
-  private def calculatePartSize(file: File) = {
+  private def calculatePartSize(path: Path) = {
-    val request = new PutObjectRequest("", "", file)
+    val request = new PutObjectRequest("", "", path.toFile)
     val configuration = new TransferManagerConfiguration
     TransferManagerUtils.calculateOptimalPartSize(request, configuration)
   }
@@ -43,11 +43,11 @@ trait ETagGenerator {
   def offsets(totalFileSizeBytes: Long, optimalPartSize: Long): List[Long] =
     Range.Long(0, totalFileSizeBytes, optimalPartSize).toList
 
-  def digestChunk(file: File, chunkSize: Long)(chunkNumber: Long)(implicit l: Logger): IO[Array[Byte]] =
+  def digestChunk(path: Path, chunkSize: Long)(chunkNumber: Long)(implicit l: Logger): IO[Array[Byte]] =
-    hashChunk(file, chunkNumber, chunkSize).map(_.digest)
+    hashChunk(path, chunkNumber, chunkSize).map(_.digest)
 
-  def hashChunk(file: File, chunkNumber: Long, chunkSize: Long)(implicit l: Logger): IO[MD5Hash] =
+  def hashChunk(path: Path, chunkNumber: Long, chunkSize: Long)(implicit l: Logger): IO[MD5Hash] =
-    MD5HashGenerator.md5FileChunk(file, chunkNumber * chunkSize, chunkSize)
+    MD5HashGenerator.md5FileChunk(path, chunkNumber * chunkSize, chunkSize)
 }
 
 object ETagGenerator extends ETagGenerator

storage-aws/src/main/scala/net/kemitix/thorp/storage/aws/S3HashService.scala

@@ -1,6 +1,6 @@
 package net.kemitix.thorp.storage.aws
 
-import java.io.File
+import java.nio.file.Path
 
 import cats.effect.IO
 import net.kemitix.thorp.core.MD5HashGenerator
@@ -12,13 +12,14 @@ trait S3HashService extends HashService {
   /**
     * Generates an MD5 Hash and an multi-part ETag
     *
-    * @param file the local file to scan
+    * @param path the local path to scan
     * @return a set of hash values
     */
-  override def hashLocalObject(file: File)(implicit l: Logger): IO[Map[String, MD5Hash]] =
+  override def hashLocalObject(path: Path)
+                              (implicit l: Logger): IO[Map[String, MD5Hash]] =
     for {
-      md5 <- MD5HashGenerator.md5File(file)
+      md5 <- MD5HashGenerator.md5File(path)
-      etag <- ETagGenerator.eTag(file).map(MD5Hash(_))
+      etag <- ETagGenerator.eTag(path).map(MD5Hash(_))
     } yield Map(
       "md5" -> md5,
       "etag" -> etag

storage-aws/src/test/scala/net/kemitix/thorp/storage/aws/ETagGeneratorTest.scala

@@ -8,6 +8,7 @@ import org.scalatest.FunSpec
 class ETagGeneratorTest extends FunSpec {
 
   private val bigFile = Resource(this, "big-file")
+  private val bigFilePath = bigFile.toPath
   private val configuration = new TransferManagerConfiguration
   private val chunkSize = 1200000
   configuration.setMinimumUploadPartSize(chunkSize)
@@ -35,7 +36,7 @@ class ETagGeneratorTest extends FunSpec {
         "8a0c1d0778ac8fcf4ca2010eba4711eb"
       ).zipWithIndex
       md5Hashes.foreach { case (hash, index) =>
-        test(hash, ETagGenerator.hashChunk(bigFile, index, chunkSize)(logger).unsafeRunSync)
+        test(hash, ETagGenerator.hashChunk(bigFilePath, index, chunkSize)(logger).unsafeRunSync)
       }
     }
   }
@@ -43,7 +44,7 @@ class ETagGeneratorTest extends FunSpec {
   describe("create etag for whole file") {
     val expected = "f14327c90ad105244c446c498bfe9a7d-2"
     it("should match aws etag for the file") {
-      val result = ETagGenerator.eTag(bigFile)(logger).unsafeRunSync
+      val result = ETagGenerator.eTag(bigFilePath)(logger).unsafeRunSync
       assertResult(expected)(result)
     }
   }

storage-aws/src/test/scala/net/kemitix/thorp/storage/aws/S3StorageServiceSuite.scala

@@ -18,8 +18,9 @@ class S3StorageServiceSuite
 
   describe("listObjectsInPrefix") {
     val source = Resource(this, "upload")
+    val sourcePath = source.toPath
     val prefix = RemoteKey("prefix")
-    implicit val config: Config = Config(Bucket("bucket"), prefix, source = source)
+    implicit val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
     implicit val implLogger: Logger = new DummyLogger
 
     val lm = LastModified(Instant.now.truncatedTo(ChronoUnit.MILLIS))

storage-aws/src/test/scala/net/kemitix/thorp/storage/aws/StorageServiceSuite.scala

@@ -18,19 +18,20 @@ class StorageServiceSuite
     with MockFactory {
 
   val source = Resource(this, "upload")
+  val sourcePath = source.toPath
 
   private val prefix = RemoteKey("prefix")
-  implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
+  implicit private val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
   implicit private val implLogger: Logger = new DummyLogger
-  private val fileToKey = KeyGenerator.generateKey(config.source, config.prefix) _
+  private val fileToKey = KeyGenerator.generateKey(config.sources, config.prefix) _
 
   describe("getS3Status") {
     val hash = MD5Hash("hash")
-    val localFile = LocalFile.resolve("the-file", md5HashMap(hash), source, fileToKey)
+    val localFile = LocalFile.resolve("the-file", md5HashMap(hash), sourcePath, fileToKey)
     val key = localFile.remoteKey
-    val keyOtherKey = LocalFile.resolve("other-key-same-hash", md5HashMap(hash), source, fileToKey)
+    val keyOtherKey = LocalFile.resolve("other-key-same-hash", md5HashMap(hash), sourcePath, fileToKey)
     val diffHash = MD5Hash("diff")
-    val keyDiffHash = LocalFile.resolve("other-key-diff-hash", md5HashMap(diffHash), source, fileToKey)
+    val keyDiffHash = LocalFile.resolve("other-key-diff-hash", md5HashMap(diffHash), sourcePath, fileToKey)
     val lastModified = LastModified(Instant.now)
     val s3ObjectsData: S3ObjectsData = S3ObjectsData(
       byHash = Map(
@@ -70,7 +71,7 @@ class StorageServiceSuite
     }
 
     describe("when remote key does not exist and no others matches hash") {
-      val localFile = LocalFile.resolve("missing-file", md5HashMap(MD5Hash("unique")), source, fileToKey)
+      val localFile = LocalFile.resolve("missing-file", md5HashMap(MD5Hash("unique")), sourcePath, fileToKey)
       it("should return no matches by key") {
         val result = getMatchesByKey(invoke(localFile))
         assert(result.isEmpty)
@@ -113,7 +114,7 @@ class StorageServiceSuite
 
       val prefix = RemoteKey("prefix")
       val localFile =
-        LocalFile.resolve("root-file", md5HashMap(Root.hash), source, KeyGenerator.generateKey(source, prefix))
+        LocalFile.resolve("root-file", md5HashMap(Root.hash), sourcePath, KeyGenerator.generateKey(config.sources, prefix))
       val bucket = Bucket("a-bucket")
       val remoteKey = RemoteKey("prefix/root-file")
       val uploadEventListener = new UploadEventListener(localFile, 1, SyncTotals(), 0L)

storage-aws/src/test/scala/net/kemitix/thorp/storage/aws/UploaderSuite.scala

@@ -16,10 +16,11 @@ class UploaderSuite
     with MockFactory {
 
   private val source = Resource(this, ".")
+  private val sourcePath = source.toPath
   private val prefix = RemoteKey("prefix")
-  implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
+  implicit private val config: Config = Config(Bucket("bucket"), prefix, sources = Sources(List(sourcePath)))
   implicit private val implLogger: Logger = new DummyLogger
-  private val fileToKey = generateKey(config.source, config.prefix) _
+  private val fileToKey = generateKey(config.sources, config.prefix) _
   val lastModified = LastModified(Instant.now())
 
   def md5HashMap(hash: MD5Hash): Map[String, MD5Hash] =
@@ -38,7 +39,7 @@ class UploaderSuite
       // dies when putObject is called
       val returnedKey = RemoteKey("returned-key")
       val returnedHash = MD5Hash("returned-hash")
-      val bigFile = LocalFile.resolve("small-file", md5HashMap(MD5Hash("the-hash")), source, fileToKey)
+      val bigFile = LocalFile.resolve("small-file", md5HashMap(MD5Hash("the-hash")), sourcePath, fileToKey)
       val uploadEventListener = new UploadEventListener(bigFile, 1, SyncTotals(), 0L)
       val amazonS3 = mock[AmazonS3]
       val amazonS3TransferManager = TransferManagerBuilder.standard().withS3Client(amazonS3).build