Create extension that can disable exec checks:

  $ cat > noexec.py <<EOF

  > from mercurial import extensions, util

  > def setflags(orig, f, l, x):

  >     pass

  > def checkexec(orig, path):

  >     return False

  > def extsetup(ui):

  >     extensions.wrapfunction(util, 'setflags', setflags)

  >     extensions.wrapfunction(util, 'checkexec', checkexec)

  > EOF

  $ hg init unix-repo

  $ cd unix-repo

  $ touch a

  $ hg add a

  $ hg commit -m 'unix: add a'

  $ hg clone . ../win-repo

  updating to branch default

  1 files updated, 0 files merged, 0 files removed, 0 files unresolved

  $ chmod +x a

  $ hg commit -m 'unix: chmod a'

  $ hg manifest -v

  755 * a

  $ cd ../win-repo

  $ touch b

  $ hg add b

  $ hg commit -m 'win: add b'

  $ hg manifest -v

  644   a

  644   b

  $ hg pull

  pulling from $TESTTMP/unix-repo

  searching for changes

  adding changesets

  adding manifests

  adding file changes

  added 1 changesets with 0 changes to 0 files (+1 heads)

  (run 'hg heads' to see heads, 'hg merge' to merge)

  $ hg manifest -v -r tip

  755 * a

Simulate a Windows merge:

  $ hg --config extensions.n=$TESTTMP/noexec.py merge --debug

    searching for copies back to rev 1

    unmatched files in local:

     b

  resolving manifests

   overwrite None partial False

   ancestor a03b0deabf2b local d6fa54f68ae1+ remote 2d8bcf2dda39

   a: update permissions -> e

  updating: a 1/1 files (100.00%)

  0 files updated, 0 files merged, 0 files removed, 0 files unresolved

  (branch merge, don't forget to commit)

Simulate a Windows commit:

  $ hg --config extensions.n=$TESTTMP/noexec.py commit -m 'win: merge'

  $ hg manifest -v

  755 * a

  644   b