diff --git a/papers/commands/edit_cmd.py b/papers/commands/edit_cmd.py
index 8bec6c9..31157f9 100644
--- a/papers/commands/edit_cmd.py
+++ b/papers/commands/edit_cmd.py
@@ -1,7 +1,7 @@
-import subprocess
-
 from ..color import colored
+from ..files import editor_input
 from .. import repo
+from ..paper import get_bibentry_from_string
 
 
 def parser(subparsers, config):
@@ -17,13 +17,32 @@ def parser(subparsers, config):
 def command(config, ui, reference):
     rp = repo.Repository.from_directory()
     key = rp.citekey_from_ref(reference, fatal=True)
+    paper = rp.paper_from_citekey(key)
     filepath = rp.path_to_paper_file(key, 'bib')
-    subprocess.call([config.get('papers', 'edit-cmd'),
-        filepath])
-    # TODO use editor_input from files.py instead of directly editing the file.
-    # Then chack that output file is correctly formmatted and that citekey has
-    # not changed or is still a valid citekey.
-    print('{} editing {}.'.format(
-        colored('Done', 'ok'),
-        colored(filepath, 'filepath')
-        ))
+    editor = config.get('papers', 'edit-cmd')
+    with open(filepath) as f:
+        content = f.read()
+    while True:
+        # Get new content from user
+        content = editor_input(editor, content)
+        # Parse new content
+        new_key, bib = get_bibentry_from_string(content)
+        paper.update(key=key, bib=bib)
+        # TODO merge into an update method
+        paper.citekey = new_key
+        paper.bibentry = bib
+        try:
+            rp.update(paper, old_citekey=key)
+            break
+        except repo.CiteKeyAlreadyExists:
+            options = ['overwrite', 'edit again', 'abort']
+            choice = options[ui.input_choice(
+                        options,
+                        ['o', 'e', 'a'],
+                        question='A paper already exist with this citekey.'
+                        )]
+            if choice == 'abort':
+                break
+            elif choice == 'overwrite':
+                rp.update(paper, old_citekey=key, overwrite=True)
+            # else edit again
diff --git a/papers/paper.py b/papers/paper.py
index 5b4ff22..941faec 100644
--- a/papers/paper.py
+++ b/papers/paper.py
@@ -42,7 +42,7 @@ def get_bibentry_from_file(bibfile):
 def get_bibentry_from_string(content):
     """Extract first entry (supposed to be the only one) from given file.
     """
-    bib_data = files.parse_bibdata(StringIO(content))
+    bib_data = files.parse_bibdata(StringIO(content), 'yml')
     first_key = bib_data.entries.keys()[0]
     first_entry = bib_data.entries[first_key]
     return first_key, first_entry
@@ -70,6 +70,12 @@ def get_safe_metadata(metapath):
         return files.read_yamlfile(metapath)
 
 
+def check_citekey(citekey):
+    # TODO This is not the right way to test that (17/12/2012)
+    if unicode(citekey) != str2citekey(citekey):
+        raise(ValueError("Invalid citekey: %s" % citekey))
+
+
 class NoDocumentFile(Exception):
     pass
 
@@ -89,9 +95,7 @@ class Paper(object):
         if not metadata:
             metadata = Paper.create_meta()
         self.metadata = metadata
-        # TODO This is not the right way to test that (17/12/2012)
-        if unicode(citekey) != str2citekey(citekey):
-            raise(ValueError("Invalid citekey: %s" % citekey))
+        check_citekey(citekey)
         self.citekey = citekey
 
     def __eq__(self, other):
@@ -158,6 +162,15 @@ class Paper(object):
         files.save_bibdata(bibdata, bib_filepath)
         files.save_meta(self.metadata, meta_filepath)
 
+    def update(self, key=None, bib=None, meta=None):
+        if key is not None:
+            check_citekey(key)
+            self.citekey = key
+        if bib is not None:
+            self.bibentry = bib
+        if meta is not None:
+            self.metadata = meta
+
     def get_document_file_from_bibdata(self, remove=False):
         """Try extracting document file from bib data.
         Raises NoDocumentFile if not found.
diff --git a/papers/repo.py b/papers/repo.py
index 985f796..f49d230 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -15,6 +15,10 @@ META_DIR = 'meta'
 DOC_DIR = 'doc'
 
 
+class CiteKeyAlreadyExists(Exception):
+    pass
+
+
 class Repository(object):
 
     def __init__(self, config=None):
@@ -86,7 +90,7 @@ class Repository(object):
     def update(self, paper, old_citekey=None, overwrite=False):
         """Updates a paper, eventually changing its citekey.
         The paper should be in repository. If the citekey changes,
-        the new citekey should be free excpet if the overwrite argumnent
+        the new citekey should be free except if the overwrite argument
         is set to True.
         """
         if old_citekey is None:
@@ -99,7 +103,7 @@ class Repository(object):
             else:
                 if self.has_paper(paper.citekey):
                     if not overwrite:
-                        raise(ValueError,
+                        raise(CiteKeyAlreadyExists,
                             "There is already a paper with citekey: %s."
                                 % paper.citekey)
                     else:
@@ -116,8 +120,9 @@ class Repository(object):
                 self.remove(old_citekey)
 
     def remove(self, citekey):
-        self.citekeys.remove(citekey)
         paper = self.paper_from_citekey(citekey)
+        self.citekeys.remove(citekey)
+        self.save()
         for f in ('bib', 'meta'):
             os.remove(self.path_to_paper_file(citekey, f))
         # Eventually remove associated document
@@ -196,7 +201,7 @@ class Repository(object):
         else:
             doc_path = self.get_document_directory()
             if not (os.path.exists(doc_path) and os.path.isdir(doc_path)):
-                raise(ValueError,
+                raise(NoDocumentFile,
                       "Document directory %s, does not exist." % doc_path)
             ext = os.path.splitext(doc_file)[1]
             new_doc_file = os.path.join(doc_path, citekey + ext)