8 files changed, 55 insertions, 10 deletions
diff --git a/Build/BundledPrograms.hs b/Build/BundledPrograms.hs
index bd1c25359..74e187618 100644
--- a/Build/BundledPrograms.hs
+++ b/Build/BundledPrograms.hs
@@ -17,7 +17,26 @@ import Build.SysConfig as SysConfig
  -
  - These may be just the command name, or the full path to it. -}
 bundledPrograms :: [FilePath]
-bundledPrograms = catMaybes
+bundledPrograms = preferredBundledPrograms ++ extraBundledPrograms
+
+{- Programs that are only included in the bundle in case the system
+ - doesn't have them. These come after the system PATH.
+ -}
+extraBundledPrograms :: [FilePath]
+extraBundledPrograms = catMaybes
+	-- The system gpg is probably better, because it may better
+	-- integrate with the system gpg-agent, etc.
+	[ SysConfig.gpg
+	]
+
+{- Programs that should be preferred for use from the bundle, over
+ - any that might be installed on the system otherwise. These come before
+ - the system PATH.
+ -
+ - For example, git-annex is built for a specific version of git.
+ -}
+preferredBundledPrograms :: [FilePath]
+preferredBundledPrograms = catMaybes
 	[ Nothing
 #ifndef mingw32_HOST_OS
 	-- git is not included in the windows bundle; git for windows is used
@@ -56,7 +75,6 @@ bundledPrograms = catMaybes
 #ifndef mingw32_HOST_OS
 	-- All these utilities are included in git for Windows
 	, ifset SysConfig.curl "curl"
-	, SysConfig.gpg
 	, SysConfig.sha1
 	, SysConfig.sha256
 	, SysConfig.sha512
diff --git a/Build/Standalone.hs b/Build/Standalone.hs
index 2a6c04e6d..a3a4bac48 100644
--- a/Build/Standalone.hs
+++ b/Build/Standalone.hs
@@ -26,6 +26,9 @@ progDir topdir = topdir
 progDir topdir = topdir </> "bin"
 #endif
 
+extraProgDir :: FilePath -> FilePath
+extraProgDir topdir = topdir </> "extra"
+
 installProg :: FilePath -> FilePath -> IO (FilePath, FilePath)
 installProg dir prog = searchPath prog >>= go
   where
@@ -41,7 +44,9 @@ main = getArgs >>= go
   where
 	go [] = error "specify topdir"
 	go (topdir:_) = do
-		let dir = progDir topdir
-		createDirectoryIfMissing True dir
-		installed <- forM bundledPrograms $ installProg dir
-		writeFile "tmp/standalone-installed" (show installed)
+		installed <- forM
+			[ (progDir topdir, preferredBundledPrograms)
+			, (extraProgDir topdir, extraBundledPrograms) ] $ \(dir, progs) -> do
+			createDirectoryIfMissing True dir
+			forM progs $ installProg dir
+		writeFile "tmp/standalone-installed" (show (concat installed))
diff --git a/debian/changelog b/debian/changelog
index 1434746f9..c1768b73e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,8 @@ git-annex (6.20160218) UNRELEASED; urgency=medium
   * fsck: When the only copy of a file is in a dead repository, mention
     the repository.
   * info: Mention when run in a dead repository.
+  * Linux and OSX standalone builds put the bundled gpg last in PATH,
+    so any system gpg will be preferred over it.
 
  -- Joey Hess <id@joeyh.name>  Thu, 18 Feb 2016 13:09:21 -0400
 
diff --git a/doc/bugs/put_gpg_last_in_OSX_dmg_PATH.mdwn b/doc/bugs/put_gpg_last_in_OSX_dmg_PATH.mdwn
index 2f30352f9..dfaec26f1 100644
--- a/doc/bugs/put_gpg_last_in_OSX_dmg_PATH.mdwn
+++ b/doc/bugs/put_gpg_last_in_OSX_dmg_PATH.mdwn
@@ -6,3 +6,5 @@ A solution might be to move the gpg binary to a different directory and put
 it at the end of PATH, not the front. So system one is used if available.
 
 This should also be considered for the linux standalone builds.
+
+> [[done]] for both OSX and linux. --[[Joey]]
diff --git a/doc/todo/cloning_direct_mode_repo_over_http/comment_1_36701696af41f8b71bb2fd4829f05b7c._comment b/doc/todo/cloning_direct_mode_repo_over_http/comment_1_36701696af41f8b71bb2fd4829f05b7c._comment
new file mode 100644
index 000000000..a1abe3f2b
--- /dev/null
+++ b/doc/todo/cloning_direct_mode_repo_over_http/comment_1_36701696af41f8b71bb2fd4829f05b7c._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2016-02-19T19:55:20Z"
+ content="""
+v6 unlocked files don't have this problem; a repo containing them can be
+accessed over http.
+
+So, I think that's a better way to go than complicating the http support
+with direct mode stuff. Especially since direct mode is going away.
+
+Won't close this yet, but will when I get around to removing direct mode..
+"""]]
diff --git a/doc/todo/git_annex_push.mdwn b/doc/todo/git_annex_push.mdwn
index 079c83e46..4abdf253c 100644
--- a/doc/todo/git_annex_push.mdwn
+++ b/doc/todo/git_annex_push.mdwn
@@ -1 +1,6 @@
 A common use case for me is to use annex as really just an addition to git to store additional content.  What I am ending up with is two stage procedure to submit my changes to our shared repository:  git push REMOTE; git annex copy --to=REMOTE . IMHO it would only be logical if there was "git annex push REMOTE [GITPUSHOPTIONS]" which would be merely an alias for "git push REMOTE [GITPUSHOPTIONS]; git annex copy --to=REMOTE" but which will make use of annex for such common usecase simple(r)
+
+> After this was opened, some options were added, so use:
+> `git-annex sync --no-pull --content`
+> 
+> [[done]] --[[Joey]] 
diff --git a/standalone/linux/skel/runshell b/standalone/linux/skel/runshell
index 8c1db4247..fff0f7082 100755
--- a/standalone/linux/skel/runshell
+++ b/standalone/linux/skel/runshell
@@ -81,10 +81,10 @@ if [ -z "$GIT_ANNEX_PACKAGE_INSTALL" ]; then
 fi
 
 # Put our binaries first, to avoid issues with out of date or incompatable
-# system binaries.
+# system binaries. Extra binaries come after system path.
 ORIG_PATH="$PATH"
 export ORIG_PATH
-PATH="$base/bin:$PATH"
+PATH="$base/bin:$PATH:$base/extra"
 export PATH
 
 # These env vars are used by the shim wrapper around each binary.
diff --git a/standalone/osx/git-annex.app/Contents/MacOS/runshell b/standalone/osx/git-annex.app/Contents/MacOS/runshell
index b48017f43..ab0076546 100755
--- a/standalone/osx/git-annex.app/Contents/MacOS/runshell
+++ b/standalone/osx/git-annex.app/Contents/MacOS/runshell
@@ -61,10 +61,10 @@ if [ ! -e "$HOME/.ssh/git-annex-wrapper" ]; then
 fi
 
 # Put our binaries first, to avoid issues with out of date or incompatable
-# system binaries.
+# system binaries. Extra binaries come after system path.
 ORIG_PATH="$PATH"
 export ORIG_PATH
-PATH="$bundle:$PATH"
+PATH="$bundle:$PATH:$base/extra"
 export PATH
 
 ORIG_GIT_EXEC_PATH="$GIT_EXEC_PATH"