Commits could be mistakenly pruned in subsequent RepoFilter().run()

[louiswpf]

Commits could be mistakenly pruned in subsequent RepoFilter().run() when using
filter-repo as a library. This is due to _SKIPPED_COMMITS not being cleared in
subsequent runs.

Here is a reproducer:

• test.py

import subprocess
from pathlib import Path

import git_filter_repo as fr

subprocess.run(["git", "init", "r0", "-q"], check=True)
(Path("r0") / "f").touch()
subprocess.run(["git", "-C", "r0", "add", "f"], check=True)
subprocess.run(["git", "-C", "r0", "commit", "-m", "c0", "-q"], check=True)

subprocess.run(["git", "init", "r1", "-q"], check=True)
for msg in ["c0", "c1"]:
  subprocess.run(
    ["git", "-C", "r1", "commit", "--allow-empty", "-m", msg, "-q"], check=True
  )

print("r1 before:")
subprocess.run(["git", "-C", "r1", "log", "--oneline"], check=True)

for repo in ["r0", "r1"]:
  print(f"_SKIPPED_COMMITS: {fr._SKIPPED_COMMITS}")
  args = fr.FilteringOptions.parse_args(
    ["-f", f"--source={repo}", f"--target={repo}", "--path=nothing", "--quiet"]
  )
  fr.RepoFilter(args).run()

print("r1 after:")
subprocess.run(["git", "-C", "r1", "log", "--oneline"], check=True)

$ python test.py
r1 before:
1c29cdf (HEAD -> main) c1
962b81e c0
_SKIPPED_COMMITS: set()
New history written in 0.01 seconds; now repacking/cleaning...
Completely finished after 0.04 seconds.
_SKIPPED_COMMITS: {1}
New history written in 0.01 seconds; now repacking/cleaning...
Completely finished after 0.04 seconds.
r1 after:
962b81e (HEAD -> main) c0