From Fedora Project Wiki

Replacing a directory or a symlink with a directory

Due to a known limitation with RPM, it is not possible to replace a directory with any kind of file or symlink, nor is it possible to replace a symlink to a directory with a directory, without RPM producing file conflict errors while trying to install the package. For more information on the issues involved, refer to bug 447156 and bug 646523.

Try to avoid the problem in the first place

While its obviously not possible to foresee all the cases where the need might arise, when the need is foreseeable, such as with bundled libraries, it'd be better to use a symlink from the start, as the symlink target can be changed more easily. For instance, if you have a bundled libfoo library inside the packages directory structure, place it in a eg. libfoo.bundled directory and make libfoo a symlink to that. When the bundling is eventually removed, you just need to drop the directory and change the symlink to point to the corresponding system library directory, without resorting to the scriptlets described below.

Working around it with scriptlets

To work around this problem, you must include a %pretrans scriptlet that manually performs the conversion prior to RPM attempting to install the package.

%pretrans scriptlets must use -p <lua> to survive initial system installation, but since there will never be transitions like these to perform on initial system installation, you can count on a shell being present when it actually performs the conversion. This means that you need to use -p <lua> in order to test if the replacement needs to be made (by examining whether the path is a directory or symlink), but you can safely shell out using os.execute() to actually perform the replacement.

Please use whichever of the two following snippets is necessary in packages that need this transition, replacing /path/to/dir with the path to the directory that is being converted.

Scriptlet to replace a directory

RPM cannot simply remove a directory when it is replaced by a file or symlink, since users may have added or modified files to the directory. To protect against accidental data loss, you must use the following scriptlet which renames the directory with a .rpmmoved suffix so that users can find the backed up directory if they need to after the package is upgraded. (It also will append an integer to the suffix in the rare event that directory also exists.)

Never use this for directories where users or other packages might add or modify files.
e.g. in subdirectories of /etc or /var or in directories where other software is expected to drop in plugins, configuration, or data.
%pretrans -p <lua>
-- Define the path to directory being replaced below.
-- DO NOT add a trailing slash at the end.
path = "/path/to/dir"
st = posix.stat(path)
if st and st.type == "directory" then
  status = os.rename(path, path .. ".rpmmoved")
  if not status then
    suffix = 0
    while not status do
      suffix = suffix + 1
      status = os.rename(path .. ".rpmmoved", path .. ".rpmmoved." .. suffix)
    os.rename(path, path .. ".rpmmoved")

Additionally, you should define the /path/to/dir.rpmmoved directory as a %ghost entry in the %files list in the package's spec file, so that the directory is not entirely orphaned and can be deleted if the package is ever uninstalled and the directory is empty.

Scriptlet to replace a symlink to a directory with a directory

Replacing a symlink to a directory with a regular directory is much simpler, since there's no potential for accidentally removing files added externally. This scriptlet check the remove the symlink (there is no need to create the directory here, rpm will do so later when it is used):

%pretrans -p <lua>
-- Define the path to the symlink being replaced below.
path = "/path/to/dir"
st = posix.stat(path)
if st and st.type == "link" then
Use this scriptlet only when replacing a symlink to a directory with a regular directory.
  • Do not use it to replace a symlink that previously pointed to a file.
  • Do not use it to replace a symlink with another symlink, even if the target is a different directory.