diff --git a/planemo/commands/cmd_project_init.py b/planemo/commands/cmd_project_init.py
index 7251a0393..4df2b68d8 100644
--- a/planemo/commands/cmd_project_init.py
+++ b/planemo/commands/cmd_project_init.py
@@ -8,6 +8,7 @@
 from planemo import options
 from planemo.cli import command_function
 from planemo.io import (
+    info,
     untar_to,
     warn,
 )
@@ -42,6 +43,7 @@ def cli(ctx, path, template=None, **kwds):
         untar_args = UNTAR_ARGS % (tempdir)
         untar_to(DOWNLOAD_URL, tempdir, untar_args)
         template_dir = os.path.join(tempdir, template)
+        info("mv '%s'/* '%s'" % (template_dir, path))
         for entry in os.listdir(template_dir):
             shutil.move(os.path.join(template_dir, entry), path)
     finally:
diff --git a/planemo/io.py b/planemo/io.py
index 3bfdd070d..0e4608bb9 100644
--- a/planemo/io.py
+++ b/planemo/io.py
@@ -45,6 +45,26 @@ def communicate(cmds, **kwds):
     return output
 
 
+def copy(source, dest):
+    info("cp '%s' '%s'" % (source, dest))
+    shutil.copy(source, dest)
+
+
+def mkdir(path):
+    info("mkdir '%s'" % path)
+    os.mkdir(path)
+
+
+def makedirs(path):
+    info("mkdir -p '%s'" % path)
+    os.makedirs(path)
+
+
+def rm_rf_tree(path):
+    info("rm -rf '%s'" % path)
+    shutil.rmtree(path, ignore_errors=True)
+
+
 def shell(cmds, **kwds):
     if isinstance(cmds, list):
         cmd_string = commands.argv_to_str(cmds)
diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py
index 298c4e937..0275e4001 100644
--- a/planemo/shed/__init__.py
+++ b/planemo/shed/__init__.py
@@ -6,7 +6,6 @@
 import json
 import os
 import re
-import shutil
 import sys
 import tarfile
 from collections import namedtuple
@@ -25,9 +24,12 @@
 from planemo.io import (
     can_write_to_path,
     coalesce_return_codes,
+    copy as io_copy,
     error,
     find_matching_directories,
     info,
+    mkdir,
+    rm_rf_tree,
     shell,
     temp_directory,
     warn,
@@ -205,7 +207,7 @@ def shed_init(ctx, path, **kwds):
         workflow_name = os.path.basename(from_workflow)
         workflow_target = os.path.join(path, workflow_name)
         if not os.path.exists(workflow_target):
-            shutil.copyfile(from_workflow, workflow_target)
+            io_copy(from_workflow, workflow_target)
 
         if not can_write_to_path(repo_dependencies_path, **kwds):
             return 1
@@ -287,7 +289,7 @@ def upload_repository(ctx, realized_repository, **kwds):
         tar_path = build_tarball(path, **kwds)
     if kwds.get("tar_only", False):
         name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
-        shutil.copy(tar_path, name)
+        io_copy(tar_path, name)
         return 0
     shed_context = get_shed_context(ctx, **kwds)
     update_kwds = {}
@@ -393,9 +395,9 @@ def _diff_in(ctx, working, realized_repository, **kwds):
         )
     else:
         tar_path = build_tarball(path)
-        os.mkdir(mine)
+        mkdir(mine)
         shell(['tar', '-xzf', tar_path, '-C', mine])
-        shutil.rmtree(tar_path, ignore_errors=True)
+        rm_rf_tree(tar_path)
 
     output = kwds.get("output", None)
     raw = kwds.get("raw", False)
diff --git a/planemo/tool_builder.py b/planemo/tool_builder.py
index 96bce16c6..3000f9927 100644
--- a/planemo/tool_builder.py
+++ b/planemo/tool_builder.py
@@ -848,7 +848,7 @@ def write_tool_description(ctx, tool_description, **kwds):
     if tool_description.test_files:
         if not os.path.exists("test-data"):
             io.info("No test-data directory, creating one.")
-            os.makedirs('test-data')
+            io.makedirs('test-data')
         for test_file in tool_description.test_files:
             io.info("Copying test-file %s" % test_file)
             try: