diff --git a/config/config.go b/config/config.go
index 5b8a9d07..bfd3fbc7 100644
--- a/config/config.go
+++ b/config/config.go
@@ -291,11 +291,12 @@ func (c *Configuration) SetEndpointAccess(e Endpoint, authType string) {
 	}
 }
 
-func (c *Configuration) FetchIncludePaths() []string {
+func (c *Configuration) GlobalFetchIncludePaths() []string {
 	c.loadGitConfig()
 	return c.fetchIncludePaths
 }
-func (c *Configuration) FetchExcludePaths() []string {
+
+func (c *Configuration) GlobalFetchExcludePaths() []string {
 	c.loadGitConfig()
 	return c.fetchExcludePaths
 }
@@ -587,20 +588,68 @@ func (c *Configuration) readGitConfig(output string, uniqRemotes map[string]bool
 
 		c.gitConfig[key] = value
 
-		if len(keyParts) == 2 && keyParts[0] == "lfs" && keyParts[1] == "fetchinclude" {
-			for _, inc := range strings.Split(value, ",") {
-				inc = strings.TrimSpace(inc)
-				c.fetchIncludePaths = append(c.fetchIncludePaths, inc)
-			}
-		} else if len(keyParts) == 2 && keyParts[0] == "lfs" && keyParts[1] == "fetchexclude" {
-			for _, ex := range strings.Split(value, ",") {
-				ex = strings.TrimSpace(ex)
-				c.fetchExcludePaths = append(c.fetchExcludePaths, ex)
+		if len(keyParts) == 2 && keyParts[0] == "lfs" {
+			switch keyParts[1] {
+			case "fetchinclude":
+				c.fetchIncludePaths = cleanPaths(value, ",")
+			case "fetchexclude":
+				c.fetchExcludePaths = cleanPaths(value, ",")
 			}
 		}
 	}
 }
 
+// FetchIncludeExcludePaths is a convenience method for returning both the
+// include and exclude path for a given set of arguments by delegating into the
+// FetchIncludePaths and FetchExcludePaths functions respectively.
+func (c *Configuration) FetchIncludeExcludePaths(include, exclude string) (includes, exclues []string) {
+	return c.FetchIncludePaths(include), c.FetchExcludePaths(exclude)
+}
+
+// FetchIncludePaths returns the comma seperated include paths contained in the
+// given argument, or the GlobalFetchIncludePaths, if none were present.
+func (c *Configuration) FetchIncludePaths(args string) (includes []string) {
+	return cleanPathsDefault(args, ",", c.GlobalFetchIncludePaths())
+}
+
+// FetchExcludePaths returns the comma seperated include paths contained in the
+// given argument, or the GlobalFetchExcludePaths, if none were present.
+func (c *Configuration) FetchExcludePaths(args string) (excludes []string) {
+	return cleanPathsDefault(args, ",", c.GlobalFetchExcludePaths())
+}
+
+// cleanPathsDefault cleans the paths contained in the given `paths` argument
+// delimited by the `delim`, argument. If an empty set is returned from that
+// split, then the fallback argument is returned instead.
+func cleanPathsDefault(paths, delim string, fallback []string) []string {
+	cleaned := cleanPaths(paths, delim)
+	if len(cleaned) == 0 {
+		return fallback
+	}
+
+	return cleaned
+}
+
+// cleanPaths splits the given `paths` argument by the delimiter argument, and
+// then "cleans" that path according to the filepath.Clean function (see
+// https://golang.org/pkg/file/filepath#Clean).
+func cleanPaths(paths, delim string) (cleaned []string) {
+	// If paths is an empty string, splitting it will yield [""], which will
+	// become the filepath ".". To avoid this, bail out if trimmed paths
+	// argument is empty.
+	if paths = strings.TrimSpace(paths); len(paths) == 0 {
+		return
+	}
+
+	for _, part := range strings.Split(paths, delim) {
+		part = strings.TrimSpace(part)
+
+		cleaned = append(cleaned, filepath.Clean(part))
+	}
+
+	return cleaned
+}
+
 func keyIsUnsafe(key string) bool {
 	for _, safe := range safeKeys {
 		if safe == key {
diff --git a/lfs/lfs.go b/lfs/lfs.go
index 530e8f30..5613d1d1 100644
--- a/lfs/lfs.go
+++ b/lfs/lfs.go
@@ -84,11 +84,11 @@ func Environ() []string {
 		fmt.Sprintf("AccessDownload=%s", config.Config.Access("download")),
 		fmt.Sprintf("AccessUpload=%s", config.Config.Access("upload")),
 	)
-	if len(config.Config.FetchExcludePaths()) > 0 {
-		env = append(env, fmt.Sprintf("FetchExclude=%s", strings.Join(config.Config.FetchExcludePaths(), ", ")))
+	if len(config.Config.GlobalFetchExcludePaths()) > 0 {
+		env = append(env, fmt.Sprintf("FetchExclude=%s", strings.Join(config.Config.GlobalFetchExcludePaths(), ", ")))
 	}
-	if len(config.Config.FetchIncludePaths()) > 0 {
-		env = append(env, fmt.Sprintf("FetchInclude=%s", strings.Join(config.Config.FetchIncludePaths(), ", ")))
+	if len(config.Config.GlobalFetchIncludePaths()) > 0 {
+		env = append(env, fmt.Sprintf("FetchInclude=%s", strings.Join(config.Config.GlobalFetchIncludePaths(), ", ")))
 	}
 	for _, ext := range config.Config.Extensions() {
 		env = append(env, fmt.Sprintf("Extension[%d]=%s", ext.Priority, ext.Name))