Match .gitignore to the pathogen repo guide

.gitignore

@@ -1,20 +1,17 @@
-# Files created by the pipeline, which we want to keep out of git
-# (or at least out of _this_ git repo).
-*data/
-*results/
-*auspice/
-*build/
-*logs/
-*benchmarks/
-*.snakemake/
+# Files created by workflows that we usually want to keep out of git
+auspice/
+builds/
+data/
+results/
+logs/
+benchmarks/
+
 # Sensitive environment variables
 environment*
+env.d/
 
-# Snakemake state dir
-/.snakemake
-
-# Local config overrides
-/config_local.yaml
+# Snakemake
+.snakemake/
 
 # For Python #
 ##############
@@ -41,3 +38,14 @@ environment*
 Icon?
 ehthumbs.db
 Thumbs.db
+*~
+
+# IDE generated files #
+######################
+.vscode/
+
+# nohup output
+nohup.out
+
+# cluster logs
+slurm-*