The different types of rebase use different ways of calculating the
patches to rebase.

'git rebase' (without -m/-i/-p) uses

  git format-patch --ignore-if-in-upstream $upstream..$orig_head

'git rebase -m' uses

  git rev-list $upstream..$orig_head

'git rebase -i' (without -p) uses

  git rev-list $upstream...$orig_head --left-right --no-merges \
          --cherry-pick | sed -n "s/^>//p"

, which could also have been written

  git rev-list $upstream...$orig_head --right-only --no-merges \
          --cherry-pick

'git rebase -p' uses

  git rev-list $upstream...$orig_head --right-only

followed by cherry-picked commits found by

  git rev-list $upstream...$orig_head --cherry-mark --right-only |
  | sed -ne "s/^=//p"

As Knut Franke reported in [1], the fact that there is no
--ignore-if-in-upstream or equivalent when using merge-based rebase
means that unnecessary conflicts can arise due to commits
cherry-picked between $orig_head and $upstream.

With all the other types, there is a different problem with the method
of calculating the commits to rebase. Copying the example history from
[1]:

      .-c
     /
a---b---d---e---f
         \
          .-g---E

Commit E is here a cherry-pick of e. If we now run 'git rebase [-i|-p]
--onto c f E', the commits to rebase will be those on E that are not
equivalent to any of those in f, which in this case would be only
'g'. Commit 'E' would thus be lost.

To solve both of the above problems, we want to find the commits in
$upstream..$orig_head that are not cherry-picked in
$orig_head..$onto. There is unfortunately no direct way of finding
these commits using 'git rev-list', so we will have to resort to using
'git cherry' and filter for lines starting with '+'. This works for
all but 'rebase -p', since 'git cherry' ignores merges.

As a side-effect, we also avoid the cost of formatting patches.

Test case updates for 'rebase -m' by Knut, the rest by Martin.

 [1] http://thread.gmane.org/gmane.comp.version-control.git/161917

Helped-by: Knut Franke <knut.fra...@gmx.de>
Signed-off-by: Martin von Zweigbergk <martin.von.zweigbe...@gmail.com>
---
 git-rebase--am.sh          |  6 ++----
 git-rebase--interactive.sh |  8 +++-----
 git-rebase--merge.sh       |  2 +-
 git-rebase.sh              | 11 ++++-------
 t/t3401-rebase-partial.sh  | 17 +++++++++++++++++
 t/t3406-rebase-message.sh  | 14 +++++++-------
 6 files changed, 34 insertions(+), 24 deletions(-)

diff --git a/git-rebase--am.sh b/git-rebase--am.sh
index 37c1b23..fe3fdd1 100644
--- a/git-rebase--am.sh
+++ b/git-rebase--am.sh
@@ -16,11 +16,9 @@ skip)
        ;;
 esac
 
-test -n "$rebase_root" && root_flag=--root
 test -n "$keep_empty" && git_am_opt="$git_am_opt --keep-empty"
-git format-patch -k --stdout --full-index --ignore-if-in-upstream \
-       --src-prefix=a/ --dst-prefix=b/ \
-       --no-renames $root_flag "$revisions" |
+generate_revisions |
+sed -e 's/\([0-9a-f]\{40\}\)/From \1 Mon Sep 17 00:00:00 2001/' |
 git am $git_am_opt --rebasing --resolvemsg="$resolvemsg" &&
 move_to_original_branch
 
diff --git a/git-rebase--interactive.sh b/git-rebase--interactive.sh
index cd5a2cc..da32ca7 100644
--- a/git-rebase--interactive.sh
+++ b/git-rebase--interactive.sh
@@ -800,10 +800,8 @@ if test -z "$rebase_root"
        # this is now equivalent to ! -z "$upstream"
 then
        shortupstream=$(git rev-parse --short $upstream)
-       revisions=$upstream...$orig_head
        shortrevisions=$shortupstream..$shorthead
 else
-       revisions=$onto...$orig_head
        shortrevisions=$shorthead
 fi
 
@@ -822,6 +820,7 @@ if test t = "$preserve_merges"
 then
        if test -z "$rebase_root"
        then
+               revisions=$upstream...$orig_head
                mkdir "$rewritten" &&
                for c in $(git merge-base --all $orig_head $upstream)
                do
@@ -829,6 +828,7 @@ then
                                die "Could not init rewritten commits"
                done
        else
+               revisions=$onto...$orig_head
                mkdir "$rewritten" &&
                echo $onto > "$rewritten"/root ||
                        die "Could not init rewritten commits"
@@ -876,9 +876,7 @@ then
                fi
        done
 else
-       git rev-list $revisions --reverse --left-right --topo-order \
-               --no-merges --cherry-pick |
-       sed -n "s/^>//p" |
+       generate_revisions |
        while read -r sha1
        do
                add_pick_line $sha1
diff --git a/git-rebase--merge.sh b/git-rebase--merge.sh
index b10f2cf..bf4ec4b 100644
--- a/git-rebase--merge.sh
+++ b/git-rebase--merge.sh
@@ -131,7 +131,7 @@ echo "$onto_name" > "$state_dir/onto_name"
 write_basic_state
 
 msgnum=0
-for cmt in `git rev-list --reverse --no-merges "$revisions"`
+for cmt in $(generate_revisions)
 do
        msgnum=$(($msgnum + 1))
        echo "$cmt" > "$state_dir/cmt.$msgnum"
diff --git a/git-rebase.sh b/git-rebase.sh
index 1cd0633..0fdff87 100755
--- a/git-rebase.sh
+++ b/git-rebase.sh
@@ -530,6 +530,10 @@ then
        GIT_PAGER='' git diff --stat --summary "$mb" "$onto"
 fi
 
+generate_revisions () {
+       git cherry $onto $orig_head $upstream | sed -ne 's/^+ //p'
+}
+
 test "$type" = interactive && run_specific_rebase
 
 # Detach HEAD and reset the tree
@@ -546,11 +550,4 @@ then
        exit 0
 fi
 
-if test -n "$rebase_root"
-then
-       revisions="$onto..$orig_head"
-else
-       revisions="$upstream..$orig_head"
-fi
-
 run_specific_rebase
diff --git a/t/t3401-rebase-partial.sh b/t/t3401-rebase-partial.sh
index 7f8693b..9c5d815 100755
--- a/t/t3401-rebase-partial.sh
+++ b/t/t3401-rebase-partial.sh
@@ -50,4 +50,21 @@ test_expect_success 'rebase ignores empty commit' '
        test $(git log --format=%s C..) = "D"
 '
 
+test_expect_success 'rebase --onto does not re-apply patches in $onto' '
+       git checkout C &&
+       test_commit C2 C.t &&
+       git checkout -B my-topic-branch master &&
+       test_commit E &&
+       git rebase --onto C2 A2 &&
+       test "$(git log --format=%s C2..)" = E
+'
+
+test_expect_success 'rebase --onto does not lose patches in $upstream' '
+       git rebase --onto A2 E &&
+       test "$(git log --format=%s A2..)" = "E
+C2
+C
+B"
+'
+
 test_done
diff --git a/t/t3406-rebase-message.sh b/t/t3406-rebase-message.sh
index 6898377..3eecc66 100755
--- a/t/t3406-rebase-message.sh
+++ b/t/t3406-rebase-message.sh
@@ -5,8 +5,10 @@ test_description='messages from rebase operation'
 . ./test-lib.sh
 
 quick_one () {
-       echo "$1" >"file$1" &&
-       git add "file$1" &&
+       fileno=$2
+       test -z "$fileno" && fileno=$1
+       echo "$1" >"file$fileno" &&
+       git add "file$fileno" &&
        test_tick &&
        git commit -m "$1"
 }
@@ -16,21 +18,19 @@ test_expect_success setup '
        git branch topic &&
        quick_one X &&
        quick_one A &&
-       quick_one B &&
+       quick_one B A &&
        quick_one Y &&
 
        git checkout topic &&
        quick_one A &&
-       quick_one B &&
+       quick_one B A &&
        quick_one Z &&
        git tag start
 
 '
 
 cat >expect <<\EOF
-Already applied: 0001 A
-Already applied: 0002 B
-Committed: 0003 Z
+Committed: 0001 Z
 EOF
 
 test_expect_success 'rebase -m' '
-- 
1.7.11.1.104.ge7b44f1

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