Fix omitted folders (#12)

* make file omission more lenient

Author: irm-codebase

copier.yaml

@@ -1,20 +1,36 @@
 # === copier settings ===
 _min_copier_version: '9.4.1'
 _subdirectory: template
+_exclude:
+    # copier defaults
+    - "copier.yaml"
+    - "copier.yaml"
+    - "~*"
+    - "*.py[co]"
+    - "__pycache__"
+    - ".git"
+    - ".DS_Store"
+    - ".svn"
+    # Do not add the dummy example when updating
+    - "{% if _copier_operation == 'update' -%}workflow/rules/dummy.smk{% endif %}"
+    - "{% if _copier_operation == 'update' -%}workflow/scripts/dummy_script.py{% endif %}"
 _skip_if_exists:
   # Respect user changes, except for a few standard files.
-  - config/*
-  - "!config/README.md"  # Necessary for the snakemake workflow catalog
-  - docs/*
-  - resources/*
-  - results/*
-  - tests/*
-  - "!tests/clio_test.py"  # Standard integration tests
-  - workflow/
-  - "!workflow/profiles"  # Profiles should be equal across projects
+  - config/**
+  - docs/**
+  - resources/**
+  - results/**
+  - tests/**
+  - workflow/**
+  - .gitignore
+  - .readthedocs.yaml
   - AUTHORS
   - CITATION.cff
   - INTERFACE.yaml
+  - mkdocs.yaml
+  - pixi.toml
+  - "!config/README.md"
+  - "!tests/clio_test.py"
 _templates_suffix: .jinja
 _answers_file: .copier-answers.yml