pre-commit: run markdown-link-check, oxipng, prettier manually

The "manual" stage in pre-commit refers to a specific hook stage designed for hooks that are not intended to run automatically during a standard git commit operation. Instead, these hooks are meant to be triggered explicitly by a user, typically when performing a full repository scan or a specific check.

This speeds up the standard `pre-commit run --all-files` run by not running these two hooks.

Both hooks are time consuming

Can run the manual hooks with:

`pre-commit run --all-files --hook-stage manual`

Add pre-commit manual stage run on CI to keep full coverage

.github/workflows/lint.yml

@@ -25,6 +25,8 @@ jobs:
           key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
       - name: Run pre-commit
         run: pre-commit run --all-files
+      - name: Run manual pre-commit hooks
+        run: pre-commit run --all-files --hook-stage manual
   ls-lint:
     name: Run ls-lint
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -26,6 +26,7 @@ repos:
         files: \.(json|md|ya?ml)$
         language: node
         additional_dependencies: ["prettier@3.6.2"]
+        stages: [manual]
   - repo: https://github.com/gitleaks/gitleaks
     rev: v8.27.2
     hooks:
@@ -39,6 +40,7 @@ repos:
         name: run oxipng
         description: use lossless compression to optimize PNG files
         args: ["--fix", "-o", "4", "--strip", "safe", "--alpha"]
+        stages: [manual]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -106,6 +108,7 @@ repos:
         name: run markdown-link-check
         description: checks hyperlinks in Markdown files
         args: [--config=.github/linters/mlc_config.json, -q]
+        stages: [manual]
         types: [markdown]
         files: \.md$
   - repo: https://github.com/rubocop/rubocop