Merge branch '1.0-maint'

# Conflicts:
#	docs/changes.rst
#	docs/usage/mount.rst.inc
#	src/borg/archive.py
#	src/borg/archiver.py
#	src/borg/fuse.py
#	src/borg/testsuite/archiver.py

18 files changed, 434 insertions, 222 deletions

diff --git a/docs/api.rst b/docs/api.rst
index 718cb58e0..31a22fbb3 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -6,63 +6,55 @@ API Documentation
     :members:
     :undoc-members:
 
-.. automodule:: borg.upgrader
-    :members:
-    :undoc-members:
-
 .. automodule:: borg.archive
     :members:
     :undoc-members:
 
-.. automodule:: borg.fuse
-    :members:
-    :undoc-members:
-
-.. automodule:: borg.platform
+.. automodule:: borg.repository
     :members:
     :undoc-members:
 
-.. automodule:: borg.locking
+.. automodule:: borg.remote
     :members:
     :undoc-members:
 
-.. automodule:: borg.shellpattern
+.. automodule:: borg.cache
     :members:
     :undoc-members:
 
-.. automodule:: borg.repository
+.. automodule:: borg.key
     :members:
     :undoc-members:
 
-.. automodule:: borg.lrucache
+.. automodule:: borg.logger
     :members:
     :undoc-members:
 
-.. automodule:: borg.remote
+.. automodule:: borg.helpers
     :members:
     :undoc-members:
 
-.. automodule:: borg.xattr
+.. automodule:: borg.locking
     :members:
     :undoc-members:
 
-.. automodule:: borg.helpers
+.. automodule:: borg.shellpattern
     :members:
     :undoc-members:
 
-.. automodule:: borg.cache
+.. automodule:: borg.lrucache
     :members:
     :undoc-members:
 
-.. automodule:: borg.key
+.. automodule:: borg.fuse
     :members:
     :undoc-members:
 
-.. automodule:: borg.logger
+.. automodule:: borg.xattr
     :members:
     :undoc-members:
 
-.. automodule:: borg.platform_darwin
+.. automodule:: borg.platform
     :members:
     :undoc-members:
 
@@ -75,7 +67,7 @@ API Documentation
     :undoc-members:
 
 .. automodule:: borg.compress
-    :members:
+    :members: get_compressor, Compressor, CompressorBase
     :undoc-members:
 
 .. automodule:: borg.chunker
@@ -85,7 +77,3 @@ API Documentation
 .. automodule:: borg.crypto
     :members:
     :undoc-members:
-
-.. automodule:: borg.platform_freebsd
-    :members:
-    :undoc-members:
diff --git a/docs/changes.rst b/docs/changes.rst
index 5267551c7..15479a5ab 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -123,6 +123,51 @@ Other changes:
   - ChunkBuffer: add test for leaving partial chunk in buffer, fixes #945
 
 
+Version 1.0.6rc1 (2016-07-10)
+-----------------------------
+
+New features:
+
+- borg check --repair: heal damaged files if missing chunks re-appear (e.g. if
+  the previously missing chunk was added again in a later backup archive),
+  #148. (*) Also improved logging.
+
+Bug fixes:
+
+- sync_dir: silence fsync() failing with EINVAL, #1287
+  Some network filesystems (like smbfs) don't support this and we use this in
+  repository code.
+- borg mount (FUSE):
+
+  - fix directories being shadowed when contained paths were also specified,
+    #1295
+  - raise I/O Error (EIO) on damaged files (unless -o allow_damaged_files is
+    used), #1302. (*)
+- borg extract: warn if a damaged file is extracted, #1299. (*)
+- Added some missing return code checks (ChunkIndex._add, hashindex_resize).
+- borg check: fix/optimize initial hash table size, avoids resize of the table.
+
+Other changes:
+
+- tests:
+
+  - add more FUSE tests, #1284
+  - deduplicate fuse (u)mount code
+  - fix borg binary test issues, #862
+- docs:
+
+  - changelog: added release dates to older borg releases
+  - fix some sphinx (docs generator) warnings, #881
+
+Notes:
+
+(*) Some features depend on information (chunks_healthy list) added to item
+metadata when a file with missing chunks was "repaired" using all-zero
+replacement chunks. The chunks_healthy list is generated since borg 1.0.4,
+thus borg can't recognize such "repaired" (but content-damaged) files if the
+repair was done with an older borg version.
+
+
 Version 1.0.5 (2016-07-07)
 --------------------------
 
@@ -247,8 +292,8 @@ Other changes:
 - add .eggs to .gitignore
 
 
-Version 1.0.3
--------------
+Version 1.0.3 (2016-05-20)
+--------------------------
 
 Bug fixes:
 
@@ -277,8 +322,8 @@ Other changes:
   - borg create help: document format tags, #894
 
 
-Version 1.0.2
--------------
+Version 1.0.2 (2016-04-16)
+--------------------------
 
 Bug fixes:
 
@@ -313,8 +358,8 @@ Other changes:
   - fix confusing usage of "repo" as archive name (use "arch")
 
 
-Version 1.0.1
--------------
+Version 1.0.1 (2016-04-08)
+--------------------------
 
 New features:
 
@@ -365,8 +410,8 @@ Other changes:
   - Document logo font. Recreate logo png. Remove GIMP logo file.
 
 
-Version 1.0.0
--------------
+Version 1.0.0 (2016-03-05)
+--------------------------
 
 The major release number change (0.x -> 1.x) indicates bigger incompatible
 changes, please read the compatibility notes, adapt / test your scripts and
@@ -449,8 +494,8 @@ Other changes:
   - FAQ: how to limit bandwidth
 
 
-Version 1.0.0rc2
-----------------
+Version 1.0.0rc2 (2016-02-28)
+-----------------------------
 
 New features:
 
@@ -491,8 +536,8 @@ Other changes:
   - "connection closed by remote": add FAQ entry and point to issue #636
 
 
-Version 1.0.0rc1
-----------------
+Version 1.0.0rc1 (2016-02-07)
+-----------------------------
 
 New features:
 
@@ -541,8 +586,8 @@ Other changes:
   - misc. updates and fixes
 
 
-Version 0.30.0
---------------
+Version 0.30.0 (2016-01-23)
+---------------------------
 
 Compatibility notes:
 
@@ -619,8 +664,8 @@ Other changes:
   - add gcc gcc-c++ to redhat/fedora/corora install docs, fixes #583
 
 
-Version 0.29.0
---------------
+Version 0.29.0 (2015-12-13)
+---------------------------
 
 Compatibility notes:
 
@@ -695,8 +740,8 @@ Other changes:
   - fix wrong installation instructions for archlinux
 
 
-Version 0.28.2
---------------
+Version 0.28.2 (2015-11-15)
+---------------------------
 
 New features:
 
@@ -719,8 +764,8 @@ Other changes:
   - minor install docs improvements
 
 
-Version 0.28.1
---------------
+Version 0.28.1 (2015-11-08)
+---------------------------
 
 Bug fixes:
 
@@ -734,8 +779,8 @@ Other changes:
 - fix build on readthedocs
 
 
-Version 0.28.0
---------------
+Version 0.28.0 (2015-11-08)
+---------------------------
 
 Compatibility notes:
 
@@ -832,8 +877,8 @@ Other changes:
   - minor development docs update
 
 
-Version 0.27.0
---------------
+Version 0.27.0 (2015-10-07)
+---------------------------
 
 New features:
 
@@ -867,8 +912,8 @@ Other changes:
   - hint to single-file pyinstaller binaries from README
 
 
-Version 0.26.1
---------------
+Version 0.26.1 (2015-09-28)
+---------------------------
 
 This is a minor update, just docs and new pyinstaller binaries.
 
@@ -880,8 +925,8 @@ This is a minor update, just docs and new pyinstaller binaries.
 Note: if you did a python-based installation, there is no need to upgrade.
 
 
-Version 0.26.0
---------------
+Version 0.26.0 (2015-09-19)
+---------------------------
 
 New features:
 
@@ -941,8 +986,8 @@ Other changes:
   - Darwin (OS X Yosemite)
 
 
-Version 0.25.0
---------------
+Version 0.25.0 (2015-08-29)
+---------------------------
 
 Compatibility notes:
 
@@ -1008,8 +1053,8 @@ Other changes:
   - split install docs into system-specific preparations and generic instructions
 
 
-Version 0.24.0
---------------
+Version 0.24.0 (2015-08-09)
+---------------------------
 
 Incompatible changes (compared to 0.23):
 
@@ -1112,8 +1157,8 @@ Other changes:
 - some easy micro optimizations
 
 
-Version 0.23.0
---------------
+Version 0.23.0 (2015-06-11)
+---------------------------
 
 Incompatible changes (compared to attic, fork related):
 
diff --git a/docs/conf.py b/docs/conf.py
index a90c8c936..516702751 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -55,6 +55,8 @@ version = sw_version.split('-')[0]
 # The full version, including alpha/beta/rc tags.
 release = version
 
+suppress_warnings = ['image.nonlocal_uri']
+
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #language = None
diff --git a/docs/resources.rst b/docs/resources.rst
index 4ae184946..2ef0f021f 100644
--- a/docs/resources.rst
+++ b/docs/resources.rst
@@ -17,21 +17,15 @@ Some of them refer to attic, but you can do the same stuff (and more) with borgb
 
 - `TW's slides for borgbackup talks / lightning talks <https://slides.com/thomaswaldmann>`_ (just grab the latest ones)
 
-- "Attic / Borg Backup" talk from GPN 2015 (video, german audio, english slides):
-  `media.ccc.de <https://media.ccc.de/browse/conferences/gpn/gpn15/gpn15-6942-attic_borg_backup.html#video>`_
-  or
-  `youtube <https://www.youtube.com/watch?v=Nb5nXEKSN-k>`_
+- `Attic / Borg Backup talk from GPN 2015 (media.ccc.de) <https://media.ccc.de/browse/conferences/gpn/gpn15/gpn15-6942-attic_borg_backup.html#video>`_
+- `Attic / Borg Backup talk from GPN 2015 (youtube) <https://www.youtube.com/watch?v=Nb5nXEKSN-k>`_
 
-- "Attic" talk from Easterhegg 2015 (video, german audio, english slides):
-  `media.ccc.de <https://media.ccc.de/v/eh15_-_49_-__-_saal_-_201504042130_-_attic_-_the_holy_grail_of_backups_-_thomas#video>`_
-  or
-  `youtube <https://www.youtube.com/watch?v=96VEAAFDtJw>`_
+- `Attic talk from Easterhegg 2015 (media.ccc.de) <https://media.ccc.de/v/eh15_-_49_-__-_saal_-_201504042130_-_attic_-_the_holy_grail_of_backups_-_thomas#video>`_
+- `Attic talk from Easterhegg 2015 (youtube) <https://www.youtube.com/watch?v=96VEAAFDtJw>`_
 
-- "Attic Backup: Mount your encrypted backups over ssh", 2014 (video, english):
-  `youtube <https://www.youtube.com/watch?v=BVXDFv9YMp8>`_
+- `Attic Backup: Mount your encrypted backups over ssh (youtube) <https://www.youtube.com/watch?v=BVXDFv9YMp8>`_
 
-- "Evolution of Borg", Oct 2015 (gource visualization of attic and borg development):
-  `youtube <https://www.youtube.com/watch?v=K4k_4wDkG6Q>`_
+- `Evolution of Borg (youtube) <https://www.youtube.com/watch?v=K4k_4wDkG6Q>`_
 
 Software
 --------
diff --git a/docs/usage/check.rst.inc b/docs/usage/check.rst.inc
index 187172ffd..17d6cf492 100644
--- a/docs/usage/check.rst.inc
+++ b/docs/usage/check.rst.inc
@@ -59,9 +59,12 @@ Second, the consistency and correctness of the archive metadata is verified:
 - Check if archive metadata chunk is present. if not, remove archive from
   manifest.
 - For all files (items) in the archive, for all chunks referenced by these
-  files, check if chunk is present (if not and we are in repair mode, replace
-  it with a same-size chunk of zeros). This requires reading of archive and
-  file metadata, but not data.
+  files, check if chunk is present.
+  If a chunk is not present and we are in repair mode, replace it with a same-size
+  replacement chunk of zeros.
+  If a previously lost chunk reappears (e.g. via a later backup) and we are in
+  repair mode, the all-zero replacement chunk will be replaced by the correct chunk.
+  This requires reading of archive and file metadata, but not data.
 - If we are in repair mode and we checked all the archives: delete orphaned
   chunks from the repo.
 - if you use a remote repo server via ssh:, the archive check is executed on
diff --git a/docs/usage/help.rst.inc b/docs/usage/help.rst.inc
index 30d8c4591..f6618b677 100644
--- a/docs/usage/help.rst.inc
+++ b/docs/usage/help.rst.inc
@@ -1,48 +1,9 @@
 .. IMPORTANT: this file is auto-generated from borg's built-in help, do not edit!
 
-.. _borg_placeholders:
-
-borg help placeholders
-~~~~~~~~~~~~~~~~~~~~~~
-::
-
-
-Repository (or Archive) URLs and --prefix values support these placeholders:
-
-{hostname}
-
-    The (short) hostname of the machine.
-
-{fqdn}
-
-    The full name of the machine.
-
-{now}
-
-    The current local date and time.
-
-{utcnow}
-
-    The current UTC date and time.
-
-{user}
-
-    The user name (or UID, if no name is available) of the user running borg.
-
-{pid}
-
-    The current process ID.
-
-Examples::
-
-    borg create /path/to/repo::{hostname}-{user}-{utcnow} ...
-    borg create /path/to/repo::{hostname}-{now:%Y-%m-%d_%H:%M:%S} ...
-    borg prune --prefix '{hostname}-' ...
 .. _borg_patterns:
 
 borg help patterns
 ~~~~~~~~~~~~~~~~~~
-::
 
 
 Exclusion patterns support four separate styles, fnmatch, shell, regular
@@ -131,3 +92,42 @@ Examples::
     sh:/home/*/.thumbnails
     EOF
     $ borg create --exclude-from exclude.txt backup /
+
+.. _borg_placeholders:
+
+borg help placeholders
+~~~~~~~~~~~~~~~~~~~~~~
+
+
+Repository (or Archive) URLs and --prefix values support these placeholders:
+
+{hostname}
+
+    The (short) hostname of the machine.
+
+{fqdn}
+
+    The full name of the machine.
+
+{now}
+
+    The current local date and time.
+
+{utcnow}
+
+    The current UTC date and time.
+
+{user}
+
+    The user name (or UID, if no name is available) of the user running borg.
+
+{pid}
+
+    The current process ID.
+
+Examples::
+
+    borg create /path/to/repo::{hostname}-{user}-{utcnow} ...
+    borg create /path/to/repo::{hostname}-{now:%Y-%m-%d_%H:%M:%S} ...
+    borg prune --prefix '{hostname}-' ...
+
diff --git a/docs/usage/mount.rst.inc b/docs/usage/mount.rst.inc
index 83310d8b5..cac84a437 100644
--- a/docs/usage/mount.rst.inc
+++ b/docs/usage/mount.rst.inc
@@ -38,6 +38,13 @@ used in fstab entries:
 To allow a regular user to use fstab entries, add the ``user`` option:
 ``/path/to/repo /mnt/point fuse.borgfs defaults,noauto,user 0 0``
 
+For mount options, see the fuse(8) manual page. Additional mount options
+supported by borg:
+
+- allow_damaged_files: by default damaged files (where missing chunks were
+  replaced with runs of zeros by borg check --repair) are not readable and
+  return EIO (I/O error). Set this option to read such files.
+
 The BORG_MOUNT_DATA_CACHE_ENTRIES environment variable is meant for advanced users
 to tweak the performance. It sets the number of cached data chunks; additional
 memory usage can be up to ~8 MiB times this number. The default is the number
diff --git a/setup.py b/setup.py
index 3e916eea0..edfa7fc03 100644
--- a/setup.py
+++ b/setup.py
@@ -187,7 +187,7 @@ class build_usage(Command):
                         params = {"topic": topic,
                                   "underline": '~' * len('borg help ' + topic)}
                         doc.write(".. _borg_{topic}:\n\n".format(**params))
-                        doc.write("borg help {topic}\n{underline}\n::\n\n".format(**params))
+                        doc.write("borg help {topic}\n{underline}\n\n".format(**params))
                         doc.write(Archiver.helptext[topic])
                 else:
                     params = {"command": command,
diff --git a/src/borg/_hashindex.c b/src/borg/_hashindex.c
index 4599fe0fa..bfa3ef09b 100644
--- a/src/borg/_hashindex.c
+++ b/src/borg/_hashindex.c
@@ -100,6 +100,8 @@ static int hashindex_delete(HashIndex *index, const void *key);
 static void *hashindex_next_key(HashIndex *index, const void *key);
 
 /* Private API */
+static void hashindex_free(HashIndex *index);
+
 static int
 hashindex_index(HashIndex *index, const void *key)
 {
@@ -148,7 +150,11 @@ hashindex_resize(HashIndex *index, int capacity)
         return 0;
     }
     while((key = hashindex_next_key(index, key))) {
-        hashindex_set(new, key, key + key_size);
+        if(!hashindex_set(new, key, key + key_size)) {
+            /* This can only happen if there's a bug in the code calculating capacity */
+            hashindex_free(new);
+            return 0;
+        }
     }
     free(index->buckets);
     index->buckets = new->buckets;
diff --git a/src/borg/archive.py b/src/borg/archive.py
index 90df7f162..b4572772d 100644
--- a/src/borg/archive.py
+++ b/src/borg/archive.py
@@ -419,6 +419,7 @@ Number of files: {0.stats.nfiles}'''.format(
         :param hardlink_masters: maps paths to (chunks, link_target) for extracting subtrees with hardlinks correctly
         :param original_path: 'path' key as stored in archive
         """
+        has_damaged_chunks = 'chunks_healthy' in item
         if dry_run or stdout:
             if 'chunks' in item:
                 for _, data in self.pipeline.fetch_many([c.id for c in item.chunks], is_preloaded=True):
@@ -426,6 +427,9 @@ Number of files: {0.stats.nfiles}'''.format(
                         sys.stdout.buffer.write(data)
                 if stdout:
                     sys.stdout.buffer.flush()
+            if has_damaged_chunks:
+                logger.warning('File %s has damaged (all-zero) chunks. Try running borg check --repair.' %
+                               remove_surrogates(item[b'path']))
             return
 
         original_path = original_path or item.path
@@ -481,6 +485,9 @@ Number of files: {0.stats.nfiles}'''.format(
                     fd.truncate(pos)
                     fd.flush()
                     self.restore_attrs(path, item, fd=fd.fileno())
+            if has_damaged_chunks:
+                logger.warning('File %s has damaged (all-zero) chunks. Try running borg check --repair.' %
+                               remove_surrogates(item.path))
             if hardlink_masters:
                 # Update master entry with extracted file path, so that following hardlinks don't extract twice.
                 hardlink_masters[item.get('source') or original_path] = (None, path)
@@ -924,7 +931,7 @@ class ArchiveChecker:
         """
         # Explicitly set the initial hash table capacity to avoid performance issues
         # due to hash table "resonance"
-        capacity = int(len(self.repository) * 1.2)
+        capacity = int(len(self.repository) * 1.35 + 1)  # > len * 1.0 / HASH_MAX_LOAD (see _hashindex.c)
         self.chunks = ChunkIndex(capacity)
         marker = None
         while True:
@@ -1033,31 +1040,53 @@ class ArchiveChecker:
                     self.repository.put(id_, cdata)
 
         def verify_file_chunks(item):
-            """Verifies that all file chunks are present
+            """Verifies that all file chunks are present.
 
-            Missing file chunks will be replaced with new chunks of the same
-            length containing all zeros.
+            Missing file chunks will be replaced with new chunks of the same length containing all zeros.
+            If a previously missing file chunk re-appears, the replacement chunk is replaced by the correct one.
             """
             offset = 0
             chunk_list = []
             chunks_replaced = False
-            for chunk_id, size, csize in item.chunks:
+            has_chunks_healthy = 'chunks_healthy' in item
+            chunks_current = item.chunks
+            chunks_healthy = item.chunks_healthy if has_chunks_healthy else chunks_current
+            assert len(chunks_current) == len(chunks_healthy)
+            for chunk_current, chunk_healthy in zip(chunks_current, chunks_healthy):
+                chunk_id, size, csize = chunk_healthy
                 if chunk_id not in self.chunks:
-                    # If a file chunk is missing, create an all empty replacement chunk
-                    logger.error('{}: Missing file chunk detected (Byte {}-{})'.format(item.path, offset, offset + size))
-                    self.error_found = chunks_replaced = True
-                    data = bytes(size)
-                    chunk_id = self.key.id_hash(data)
-                    cdata = self.key.encrypt(Chunk(data))
-                    csize = len(cdata)
-                    add_reference(chunk_id, size, csize, cdata)
+                    # a chunk of the healthy list is missing
+                    if chunk_current == chunk_healthy:
+                        logger.error('{}: New missing file chunk detected (Byte {}-{}). '
+                                     'Replacing with all-zero chunk.'.format(item.path, offset, offset + size))
+                        self.error_found = chunks_replaced = True
+                        data = bytes(size)
+                        chunk_id = self.key.id_hash(data)
+                        cdata = self.key.encrypt(Chunk(data))
+                        csize = len(cdata)
+                        add_reference(chunk_id, size, csize, cdata)
+                    else:
+                        logger.info('{}: Previously missing file chunk is still missing (Byte {}-{}). It has a '
+                                    'all-zero replacement chunk already.'.format(item.path, offset, offset + size))
+                        chunk_id, size, csize = chunk_current
+                        add_reference(chunk_id, size, csize)
                 else:
-                    add_reference(chunk_id, size, csize)
-                chunk_list.append((chunk_id, size, csize))
+                    if chunk_current == chunk_healthy:
+                        # normal case, all fine.
+                        add_reference(chunk_id, size, csize)
+                    else:
+                        logger.info('{}: Healed previously missing file chunk! '
+                                    '(Byte {}-{}).'.format(item.path, offset, offset + size))
+                        add_reference(chunk_id, size, csize)
+                        mark_as_possibly_superseded(chunk_current[0])  # maybe orphaned the all-zero replacement chunk
+                chunk_list.append([chunk_id, size, csize])  # list-typed element as chunks_healthy is list-of-lists
                 offset += size
-            if chunks_replaced and 'chunks_healthy' not in item:
+            if chunks_replaced and not has_chunks_healthy:
                 # if this is first repair, remember the correct chunk IDs, so we can maybe heal the file later
                 item.chunks_healthy = item.chunks
+            if has_chunks_healthy and chunk_list == chunks_healthy:
+                logger.info('{}: Completely healed previously damaged file!'.format(item.path))
+                del item.chunks_healthy
             item.chunks = chunk_list
 
         def robust_iterator(archive):
diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index d010022a1..b2e98fb6e 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -1134,8 +1134,7 @@ class Archiver:
             re:^/home/[^/]\.tmp/
             sh:/home/*/.thumbnails
             EOF
-            $ borg create --exclude-from exclude.txt backup /
-        ''')
+            $ borg create --exclude-from exclude.txt backup /\n\n''')
     helptext['placeholders'] = textwrap.dedent('''
         Repository (or Archive) URLs and --prefix values support these placeholders:
 
@@ -1167,8 +1166,7 @@ class Archiver:
 
             borg create /path/to/repo::{hostname}-{user}-{utcnow} ...
             borg create /path/to/repo::{hostname}-{now:%Y-%m-%d_%H:%M:%S} ...
-            borg prune --prefix '{hostname}-' ...
-        ''')
+            borg prune --prefix '{hostname}-' ...\n\n''')
 
     def do_help(self, parser, commands, args):
         if not args.topic:
@@ -1331,9 +1329,12 @@ class Archiver:
         - Check if archive metadata chunk is present. if not, remove archive from
           manifest.
         - For all files (items) in the archive, for all chunks referenced by these
-          files, check if chunk is present (if not and we are in repair mode, replace
-          it with a same-size chunk of zeros). This requires reading of archive and
-          file metadata, but not data.
+          files, check if chunk is present.
+          If a chunk is not present and we are in repair mode, replace it with a same-size
+          replacement chunk of zeros.
+          If a previously lost chunk reappears (e.g. via a later backup) and we are in
+          repair mode, the all-zero replacement chunk will be replaced by the correct chunk.
+          This requires reading of archive and file metadata, but not data.
         - If we are in repair mode and we checked all the archives: delete orphaned
           chunks from the repo.
         - if you use a remote repo server via ssh:, the archive check is executed on
@@ -1739,6 +1740,13 @@ class Archiver:
         To allow a regular user to use fstab entries, add the ``user`` option:
         ``/path/to/repo /mnt/point fuse.borgfs defaults,noauto,user 0 0``
 
+        For mount options, see the fuse(8) manual page. Additional mount options
+        supported by borg:
+
+        - allow_damaged_files: by default damaged files (where missing chunks were
+          replaced with runs of zeros by borg check --repair) are not readable and
+          return EIO (I/O error). Set this option to read such files.
+
         The BORG_MOUNT_DATA_CACHE_ENTRIES environment variable is meant for advanced users
         to tweak the performance. It sets the number of cached data chunks; additional
         memory usage can be up to ~8 MiB times this number. The default is the number
diff --git a/src/borg/fuse.py b/src/borg/fuse.py
index eeb4c7f80..93530f892 100644
--- a/src/borg/fuse.py
+++ b/src/borg/fuse.py
@@ -14,7 +14,7 @@ from .logger import create_logger
 logger = create_logger()
 
 from .archive import Archive
-from .helpers import daemonize
+from .helpers import daemonize, safe_encode
 from .item import Item
 from .lrucache import LRUCache
 
@@ -50,6 +50,9 @@ class ItemCache:
 class FuseOperations(llfuse.Operations):
     """Export archive as a fuse filesystem
     """
+
+    allow_damaged_files = False
+
     def __init__(self, key, repository, manifest, archive, cached_repo):
         super().__init__()
         self._inode_count = 0
@@ -79,6 +82,32 @@ class FuseOperations(llfuse.Operations):
                 self.contents[1][os.fsencode(archive_name)] = archive_inode
                 self.pending_archives[archive_inode] = Archive(repository, key, manifest, archive_name)
 
+    def mount(self, mountpoint, mount_options, foreground=False):
+        """Mount filesystem on *mountpoint* with *mount_options*."""
+        options = ['fsname=borgfs', 'ro']
+        if mount_options:
+            options.extend(mount_options.split(','))
+        try:
+            options.remove('allow_damaged_files')
+            self.allow_damaged_files = True
+        except ValueError:
+            pass
+        llfuse.init(self, mountpoint, options)
+        if not foreground:
+            daemonize()
+
+        # If the file system crashes, we do not want to umount because in that
+        # case the mountpoint suddenly appears to become empty. This can have
+        # nasty consequences, imagine the user has e.g. an active rsync mirror
+        # job - seeing the mountpoint empty, rsync would delete everything in the
+        # mirror.
+        umount = False
+        try:
+            signal = fuse_main()
+            umount = (signal is None)  # no crash and no signal -> umount request
+        finally:
+            llfuse.close(umount)
+
     def process_archive(self, archive, prefix=[]):
         """Build fuse inode hierarchy from archive metadata
         """
@@ -88,6 +117,16 @@ class FuseOperations(llfuse.Operations):
             unpacker.feed(data)
             for item in unpacker:
                 item = Item(internal_dict=item)
+                try:
+                    # This can happen if an archive was created with a command line like
+                    # $ borg create ... dir1/file dir1
+                    # In this case the code below will have created a default_dir inode for dir1 already.
+                    inode = self._find_inode(safe_encode(item.path), prefix)
+                except KeyError:
+                    pass
+                else:
+                    self.items[inode] = item
+                    continue
                 segments = prefix + os.fsencode(os.path.normpath(item.path)).split(b'/')
                 del item.path
                 num_segments = len(segments)
@@ -214,6 +253,15 @@ class FuseOperations(llfuse.Operations):
         return self.getattr(inode)
 
     def open(self, inode, flags, ctx=None):
+        if not self.allow_damaged_files:
+            item = self.get_item(inode)
+            if 'chunks_healthy' in item:
+                # Processed archive items don't carry the path anymore; for converting the inode
+                # to the path we'd either have to store the inverse of the current structure,
+                # or search the entire archive. So we just don't print it. It's easy to correlate anyway.
+                logger.warning('File has damaged (all-zero) chunks. Try running borg check --repair. '
+                               'Mount with allow_damaged_files to read damaged files.')
+                raise llfuse.FUSEError(errno.EIO)
         return inode
 
     def opendir(self, inode, ctx=None):
@@ -254,23 +302,3 @@ class FuseOperations(llfuse.Operations):
     def readlink(self, inode, ctx=None):
         item = self.get_item(inode)
         return os.fsencode(item.source)
-
-    def mount(self, mountpoint, extra_options, foreground=False):
-        options = ['fsname=borgfs', 'ro']
-        if extra_options:
-            options.extend(extra_options.split(','))
-        llfuse.init(self, mountpoint, options)
-        if not foreground:
-            daemonize()
-
-        # If the file system crashes, we do not want to umount because in that
-        # case the mountpoint suddenly appears to become empty. This can have
-        # nasty consequences, imagine the user has e.g. an active rsync mirror
-        # job - seeing the mountpoint empty, rsync would delete everything in the
-        # mirror.
-        umount = False
-        try:
-            signal = fuse_main()
-            umount = (signal is None)  # no crash and no signal -> umount request
-        finally:
-            llfuse.close(umount)
diff --git a/src/borg/hashindex.pyx b/src/borg/hashindex.pyx
index 724f2ee84..389cf2563 100644
--- a/src/borg/hashindex.pyx
+++ b/src/borg/hashindex.pyx
@@ -18,8 +18,6 @@ cdef extern from "_hashindex.c":
     HashIndex *hashindex_read(char *path)
     HashIndex *hashindex_init(int capacity, int key_size, int value_size)
     void hashindex_free(HashIndex *index)
-    void hashindex_merge(HashIndex *index, HashIndex *other)
-    void hashindex_add(HashIndex *index, void *key, void *value)
     int hashindex_get_size(HashIndex *index)
     int hashindex_write(HashIndex *index, char *path)
     void *hashindex_get(HashIndex *index, void *key)
@@ -323,7 +321,8 @@ cdef class ChunkIndex(IndexBase):
             values[1] = data[1]
             values[2] = data[2]
         else:
-            hashindex_set(self.index, key, data)
+            if not hashindex_set(self.index, key, data):
+                raise Exception('hashindex_set failed')
 
     def merge(self, ChunkIndex other):
         cdef void *key = NULL
diff --git a/src/borg/helpers.py b/src/borg/helpers.py
index cf4d14e05..401f1ea7c 100644
--- a/src/borg/helpers.py
+++ b/src/borg/helpers.py