git clone: fall back to native git binary

On Debian 8, using git from the Alpine chroot does not work properly.
With this commit, pmbootstrap will fall back to the native git binary
for the clone.

Details:
* new function pmb.helpers.git.clone_outside()
* add docstrings to pmb.helpers.git.clone() and clone_outside()
* show the git output to the terminal in both functions, so the user
  better knows what's going on

pmb/helpers/git.py

@@ -18,6 +18,8 @@ along with pmbootstrap.  If not, see <http://www.gnu.org/licenses/>.
 """
 import logging
 import os
+import shutil
+import tempfile
 
 import pmb.build
 import pmb.chroot.apk
@@ -25,7 +27,51 @@ import pmb.config
 import pmb.helpers.run
 
 
+def clone_outside(args, options, name_repo, name_temp, chown_to_user):
+    """
+    Use the host system's git program as fallback for cloning a git repository.
+
+    :param options: list of git options, e.g. ["--depth=1"] or []
+    :param name_repo: the repositories name from pmb.config.git_repos
+    :param name_temp: the temporary name to which the repo will be cloned
+    :param chown_to_user: change ownership to the host system's user
+    """
+    logging.info("NOTE: failed to clone with git inside Alpine's chroot. This"
+                 " may happen with some host kernels (pmbootstrap#1662)."
+                 " Trying again with the host system's git binary.")
+
+    # Make sure we have git
+    if not shutil.which("git"):
+        logging.info("Please install 'git' on your host system's Linux"
+                     " distribution with its package manager and try again.")
+        raise RuntimeError("Failed to clone with git inside Alpine's chroot,"
+                           " and git is not installed in the host system.")
+
+    # Clone to temporary folder
+    tempdir = tempfile.mkdtemp(prefix="pmbootstrap_git_clone_temp")
+    url = pmb.config.git_repos[name_repo]
+    pmb.helpers.run.user(args, ["git", "-C", tempdir] + options + ["clone",
+                         url, name_temp], output="stdout")
+    # Move to pmaports folder
+    pmb.helpers.run.root(args, ["mv", tempdir + "/" + name_temp, args.work +
+                                "/cache_git/"])
+
+    # Chown to the chroot's pmos user
+    if not chown_to_user:
+        pmb.chroot.root(args, ["chown", "-R", "pmos:users", "/home/pmos/git/" +
+                               name_temp])
+
+
 def clone(args, name_repo, shallow=True, chown_to_user=False):
+    """
+    Clone a git repository from the config to $work/cache_git using the git
+    program from the native chroot.
+
+    :param name_repo: the repositories name from pmb.config.git_repos
+    :param shallow: only clone the latest revision, not the entire git history
+                    (less traffic)
+    :param chown_to_user: change ownership to the host system's user
+    """
     # Check for repo name in the config
     if name_repo not in pmb.config.git_repos:
         raise ValueError("No git repository configured for " + name_repo)
@@ -49,7 +95,10 @@ def clone(args, name_repo, shallow=True, chown_to_user=False):
         # Run the command
         pmb.chroot.user(args, ["git", "clone"] + options +
                               [pmb.config.git_repos[name_repo], name_temp],
-                        working_dir="/home/pmos/git/")
+                        working_dir="/home/pmos/git/", check=False,
+                        output="stdout")
+        if not os.path.exists(args.work + "/cache_git/" + name_temp):
+            clone_outside(args, options, name_repo, name_temp, chown_to_user)
 
     # Chown to user's UID and GID
     if chown_to_user: