diff --git a/.hgtags b/.hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -50,3 +50,4 @@ 4b34ce0d2c3c10510626b3b65044939bb7a2cddf
 14502561d22e6b70613674cd675ae9a604b7989f v4.15.1
 4aaa40b605b01af78a9f6882eca561c54b525ef0 v4.15.2
 797744642eca86640ed20bef2cd77445780abaec v4.16.0
+6c3452c7c25ed35ff269690929e11960ed6ad7d3 v4.16.1
diff --git a/docs/release-notes/release-notes-4.16.1.rst b/docs/release-notes/release-notes-4.16.1.rst
new file mode 100644
--- /dev/null
+++ b/docs/release-notes/release-notes-4.16.1.rst
@@ -0,0 +1,47 @@
+|RCE| 4.16.1 |RNS|
+------------------
+
+Release Date
+^^^^^^^^^^^^
+
+- 2019-03-07
+
+
+New Features
+^^^^^^^^^^^^
+
+
+
+General
+^^^^^^^
+
+- Docs: added missing reference for the user bookmarks feature.
+
+
+Security
+^^^^^^^^
+
+- Comments: prevent from allowing to resolve TODO comments across projects. In certain
+  conditions users could resolve TODOs not belonging to the same project.
+
+
+Performance
+^^^^^^^^^^^
+
+
+
+Fixes
+^^^^^
+
+- Downloads: fixed archive links from file tree view.
+- Markdown: fixed sanitization of checkbox extensions that removed "checked" attribute.
+- Upgrade: fixed upgrades from older versions of RhodeCode.
+- Pull Requests: handle non-ascii branches from short branch selector via URL.
+- Hooks: fixed again unicode problems with new pull request link generator.
+
+
+
+Upgrade notes
+^^^^^^^^^^^^^
+
+- Scheduled release addressing problems in 4.16.X releases.
diff --git a/docs/release-notes/release-notes.rst b/docs/release-notes/release-notes.rst
--- a/docs/release-notes/release-notes.rst
+++ b/docs/release-notes/release-notes.rst
@@ -9,6 +9,7 @@ Release Notes
 .. toctree::
    :maxdepth: 1
 
+   release-notes-4.16.1.rst
    release-notes-4.16.0.rst
    release-notes-4.15.2.rst
    release-notes-4.15.1.rst
diff --git a/rhodecode/lib/bleach_whitelist.py b/rhodecode/lib/bleach_whitelist.py
--- a/rhodecode/lib/bleach_whitelist.py
+++ b/rhodecode/lib/bleach_whitelist.py
@@ -70,7 +70,7 @@ markdown_attrs = {
     "abbr": ["title"],
     "acronym": ["title"],
     "pre": ["lang"],
-    "input": ["type", "disabled"]
+    "input": ["type", "disabled", "checked"]
 }
 
 standard_styles = [
diff --git a/rhodecode/lib/hooks_base.py b/rhodecode/lib/hooks_base.py
--- a/rhodecode/lib/hooks_base.py
+++ b/rhodecode/lib/hooks_base.py
@@ -270,7 +270,7 @@ def post_push(extras):
     # make lock is a tri state False, True, None. We only release lock on False
     if extras.make_lock is False and not is_shadow_repo(extras):
         Repository.unlock(Repository.get_by_repo_name(extras.repository))
-        msg = 'Released lock on repo `%s`\n' % extras.repository
+        msg = 'Released lock on repo `{}`\n'.format(safe_str(extras.repository))
         output += msg
 
     if extras.locked_by[0]:
@@ -284,8 +284,8 @@ def post_push(extras):
             output += _http_ret.title
 
     if extras.new_refs:
-        tmpl = extras.server_url + '/' + extras.repository + \
-               "/pull-request/new?{ref_type}={ref_name}"
+        tmpl = '{}/{}/pull-request/new?{{ref_type}}={{ref_name}}'.format(
+            safe_str(extras.server_url), safe_str(extras.repository))
 
         for branch_name in extras.new_refs['branches']:
             output += 'RhodeCode: open pull request link: {}\n'.format(
diff --git a/rhodecode/lib/markdown_ext.py b/rhodecode/lib/markdown_ext.py
--- a/rhodecode/lib/markdown_ext.py
+++ b/rhodecode/lib/markdown_ext.py
@@ -18,26 +18,11 @@
 # RhodeCode Enterprise Edition, including its added features, Support services,
 # and proprietary license terms, please see https://rhodecode.com/licenses/
 
-import re
-
 import markdown
 
 from mdx_gfm import GithubFlavoredMarkdownExtension  # pragma: no cover
 
 
-class FlavoredCheckboxPostprocessor(markdown.postprocessors.Postprocessor):
-    """
-    Adds `flavored_checkbox_list` class to list of checkboxes
-    """
-
-    pattern = re.compile(r'^([*-]) \[([ x])\]')
-
-    def run(self, html):
-        before = '<ul>\n<li><input type="checkbox"'
-        after = '<ul class="flavored_checkbox_list">\n<li><input type="checkbox"'
-        return html.replace(before, after)
-
-
 # Global Vars
 URLIZE_RE = '(%s)' % '|'.join([
     r'<(?:f|ht)tps?://[^>]*>',
diff --git a/rhodecode/lib/paster_commands/upgrade_db.py b/rhodecode/lib/paster_commands/upgrade_db.py
--- a/rhodecode/lib/paster_commands/upgrade_db.py
+++ b/rhodecode/lib/paster_commands/upgrade_db.py
@@ -26,7 +26,8 @@ log = logging.getLogger(__name__)
 
 
 class UpgradeDb(BasePasterCommand):
-    """Command used for paster to upgrade our database to newer version
+    """
+    Command used for paster to upgrade our database to newer version
     """
 
     max_args = 1
@@ -41,7 +42,7 @@ class UpgradeDb(BasePasterCommand):
     def command(self):
         from rhodecode.lib.rc_commands import upgrade_db
         upgrade_db.command(
-            self.path_to_ini_file, self.options.__dict__.get('force_ask'))
+            self.path_to_ini_file, self.options.__dict__.get('force_ask'), None)
 
     def update_parser(self):
         self.parser.add_option('--sql',
diff --git a/rhodecode/model/pull_request.py b/rhodecode/model/pull_request.py
--- a/rhodecode/model/pull_request.py
+++ b/rhodecode/model/pull_request.py
@@ -1420,8 +1420,8 @@ class PullRequestModel(BaseModel):
         _ = translator or get_current_request().translate
 
         commit_id = safe_str(commit_id) if commit_id else None
-        branch = safe_str(branch) if branch else None
-        bookmark = safe_str(bookmark) if bookmark else None
+        branch = safe_unicode(branch) if branch else None
+        bookmark = safe_unicode(bookmark) if bookmark else None
 
         selected = None
 
@@ -1439,10 +1439,11 @@ class PullRequestModel(BaseModel):
         )
 
         groups = []
+
         for group_key, ref_list, group_name, match in sources:
             group_refs = []
             for ref_name, ref_id in ref_list:
-                ref_key = '%s:%s:%s' % (group_key, ref_name, ref_id)
+                ref_key = u'{}:{}:{}'.format(group_key, ref_name, ref_id)
                 group_refs.append((ref_key, ref_name))
 
                 if not selected:
@@ -1456,11 +1457,11 @@ class PullRequestModel(BaseModel):
             ref = commit_id or branch or bookmark
             if ref:
                 raise CommitDoesNotExistError(
-                    'No commit refs could be found matching: %s' % ref)
+                    u'No commit refs could be found matching: {}'.format(ref))
             elif repo.DEFAULT_BRANCH_NAME in repo.branches:
-                selected = 'branch:%s:%s' % (
-                    repo.DEFAULT_BRANCH_NAME,
-                    repo.branches[repo.DEFAULT_BRANCH_NAME]
+                selected = u'branch:{}:{}'.format(
+                    safe_unicode(repo.DEFAULT_BRANCH_NAME),
+                    safe_unicode(repo.branches[repo.DEFAULT_BRANCH_NAME])
                 )
             elif repo.commit_ids:
                 # make the user select in this case
diff --git a/rhodecode/templates/files/files_browser.mako b/rhodecode/templates/files/files_browser.mako
--- a/rhodecode/templates/files/files_browser.mako
+++ b/rhodecode/templates/files/files_browser.mako
@@ -30,7 +30,7 @@
             % if c.enable_downloads:
               <% at_path = '{}.zip'.format(request.GET.get('at') or c.commit.raw_id[:6]) %>
               <div title="${_('Download tree at {}').format(at_path)}" class="btn btn-default new-file">
-                <a href="${h.route_path('repo_archivefile',repo_name=c.repo_name, fname=c.commit.raw_id)}">
+                <a href="${h.route_path('repo_archivefile',repo_name=c.repo_name, fname='{}.zip'.format(c.commit.raw_id))}">
                     ${_('Download tree at {}').format(at_path)}
                 </a>
               </div>