Fix: prune command must only remove directories

The issue was found in the nightly builds.

Author: ysbaddaden

src/commands/prune.cr

@@ -9,7 +9,7 @@ module Shards
         return unless lockfile?
 
         Dir[File.join(Shards.install_path, "*")].each do |path|
-          next unless Dir.exists?(path)
+          next unless File.directory?(path)
           name = File.basename(path)
 
           if locks.none? { |d| d.name == name }

test/integration/prune_test.cr

@@ -26,9 +26,9 @@ class PruneCommandTest < Minitest::Test
   end
 
   def test_wont_remove_files
-    File.write(File.join(application_path, "lib", ".keep"), "")
+    File.write(File.join(application_path, "lib", "keep"), "")
     Dir.cd(application_path) { run "shards prune" }
-    assert_equal [".keep", "web"], installed_dependencies.sort
+    assert_equal ["keep", "web"], installed_dependencies.sort
   end
 
   private def installed_dependencies