Dont remove the output folder if it's the source one ;)

bin/pelican

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 import argparse
 
-from pelican.utils import clean_output_dir
 from pelican.generators import Generator
 from pelican.processors import (ArticlesProcessor, PagesProcessor, 
                                 StaticProcessor, PdfProcessor)
@@ -30,7 +29,6 @@ if __name__ == '__main__':
 
     generator = Generator(args.settings, args.path, args.theme, 
                           args.output, markup)
-    clean_output_dir(generator.output_path)
 
     processors = [ArticlesProcessor, PagesProcessor, StaticProcessor]
     if generator.settings['PDF_PROCESSOR']:

pelican/generators.py

@@ -7,6 +7,7 @@ from jinja2.exceptions import TemplateNotFound
 from feedgenerator import Atom1Feed
 
 from pelican.settings import read_settings
+from pelican.utils import clean_output_dir
 
 _TEMPLATES = ('index', 'tag', 'tags', 'article', 'category', 'categories',
               'archives', 'page')
@@ -52,6 +53,9 @@ class Generator(object):
             if hasattr(p, 'preprocess'):
                 p.preprocess(context, self)
 
+        if self.output_path not in os.path.realpath(self.path):
+            clean_output_dir(self.output_path)
+
         for p in processors:
             p.process(context, self)