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Gitlab cache configuration (as documented) leads to corrupted/invalid cache #625

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@unode
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Following from the discussion at pre-commit/pre-commit#1133 , following the current documentation on how to configure GitLab's cache will result in errors such as:

An error has occurred: InvalidManifestError: 
=====> /builds/kjfMHq72/0/owner/project/.cache/pre-commit/repoxhyml2wy/.pre-commit-hooks.yaml is not a file
Check the log at /builds/rZMs1Hzd/0/owner/project/.cache/pre-commit/pre-commit.log

This usually happens some days/weeks after the cache was first created.
The issue can be temporarily solved by clicking the Clearing runner caches button in GitLab's CI/CD section but a more reliable solution is desirable.

pre-commit --version

2.17.0

.pre-commit-config.yaml

---
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.0.1
    hooks:
      - id: trailing-whitespace
        args: ["--markdown-linebreak-ext=md"]
      - id: end-of-file-fixer
      - id: fix-byte-order-marker
      - id: fix-encoding-pragma
        args: ["--remove"]
      - id: check-executables-have-shebangs
      - id: check-yaml
        # Allows use of !reference in .gitlab-ci.yml
        args: ["--unsafe"]
      - id: check-symlinks
      - id: check-docstring-first
      - id: check-added-large-files
      - id: check-merge-conflict
      - id: debug-statements
  - repo: https://github.com/pycqa/isort
    # Formats, sorts and reorganizes imports
    rev: 5.9.1
    hooks:
      - id: isort
        args:
          - "--profile"
          - "black"
          - "--filter-files"
          - "--thirdparty"
          - "mmpy_bot"
  - repo: https://github.com/psf/black
    # Code style formatting
    rev: 20.8b1
    hooks:
      - id: black
  - repo: https://github.com/pre-commit/mirrors-mypy
    # static type analysis
    rev: v0.812
    hooks:
      - id: mypy
  - repo: https://gitlab.com/pycqa/flake8
    # Checks the code for PEP8 violations and common pitfals
    rev: 3.9.0
    hooks:
      - id: flake8
        args:
          - "--extend-ignore"
          - "W503,E203,E501"
          - "--per-file-ignores"
          - "alembic/versions/*:E501"
  - repo: https://github.com/myint/docformatter
    # Formats docstrings following PEP 257
    rev: v1.3.1
    hooks:
      - id: docformatter
        args:
          - "--in-place"
  - repo: https://github.com/asottile/pyupgrade
    # updates syntax to use constructs introduced in newer python versions
    # e.g. f-strings instead of "{}".format()
    rev: v2.13.0
    hooks:
      - id: pyupgrade
        args:
          - --py39-plus
  - repo: https://github.com/jackdewinter/pymarkdown
    rev: 0.9.1
    hooks:
      - id: pymarkdown
        args:
          # Disable line length rule and mandatory H1 at top-level
          - --disable-rules=md013,md041
          - scan
  - repo: https://github.com/adrienverge/yamllint.git
    # validates YAML syntax
    rev: v1.26.1
    hooks:
      - id: yamllint
        args:
          - "--config-file"
          - ".yamllint.yaml"
          - "--format"
          - "parsable"
          - "--strict"
  - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
    # formats YAML to correct indentation and alignment
    rev: 0.1.0
    hooks:
      - id: yamlfmt
        args:
          - "--preserve-quotes"
          - "--mapping"
          - "2"
          - "--sequence"
          - "4"
          - "--offset"
          - "2"
  - repo: https://github.com/pycqa/doc8
    # sphinx rst style checker
    rev: 0.9.0a1
    hooks:
      - id: doc8

~/.cache/pre-commit/pre-commit.log (if present)

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