diff --git a/.flox/env/manifest.lock b/.flox/env/manifest.lock
index ae587cde..622e1ecf 100644
--- a/.flox/env/manifest.lock
+++ b/.flox/env/manifest.lock
@@ -117,7 +117,7 @@
       }
     },
     "hook": {
-      "on-activate": "if [[ -f .env ]]; then\n  while IFS= read -r line || [[ -n \"$line\" ]]; do\n    if [[ -z \"${line// /}\" ]]; then\n      continue\n    fi\n\n    if [[ \"$line\" =~ ^[[:space:]]*# ]]; then\n      continue\n    fi\n\n    line=\"${line%%[[:space:]]*#*}\"\n\n    if [[ \"$line\" =~ = ]]; then\n      key=\"${line%%=*}\"\n      value=\"${line#*=}\"\n\n      key=\"${key#\"${key%%[![:space:]]*}\"}\"  # trim leading\n      key=\"${key%\"${key##*[![:space:]]}\"}\"  # trim trailing\n\n      if [[ \"$key\" =~ ^[a-zA-Z_][a-zA-Z0-9_]*$ ]]; then\n        export \"$key=$value\"\n      else\n        echo \"Skipping invalid key '$key' in .env\" >&2\n      fi\n    fi\n  done < .env\nelse\n  echo \".env file not found, skipping environment variable loading\" >&2\nfi\n"
+      "on-activate": "if [[ -f .env ]]; then\n  set -a\n  source .env\n  set +a\nfi\n"
     },
     "options": {
       "systems": [
diff --git a/.flox/env/manifest.toml b/.flox/env/manifest.toml
index 4add0d63..bab9f242 100644
--- a/.flox/env/manifest.toml
+++ b/.flox/env/manifest.toml
@@ -46,33 +46,9 @@ markdownlint-cli.pkg-path = "markdownlint-cli"
 [hook]
 on-activate = '''
 if [[ -f .env ]]; then
-  while IFS= read -r line || [[ -n "$line" ]]; do
-    if [[ -z "${line// /}" ]]; then
-      continue
-    fi
-
-    if [[ "$line" =~ ^[[:space:]]*# ]]; then
-      continue
-    fi
-
-    line="${line%%[[:space:]]*#*}"
-
-    if [[ "$line" =~ = ]]; then
-      key="${line%%=*}"
-      value="${line#*=}"
-
-      key="${key#"${key%%[![:space:]]*}"}"  # trim leading
-      key="${key%"${key##*[![:space:]]}"}"  # trim trailing
-
-      if [[ "$key" =~ ^[a-zA-Z_][a-zA-Z0-9_]*$ ]]; then
-        export "$key=$value"
-      else
-        echo "Skipping invalid key '$key' in .env" >&2
-      fi
-    fi
-  done < .env
-else
-  echo ".env file not found, skipping environment variable loading" >&2
+  set -a
+  source .env
+  set +a
 fi
 '''
 
diff --git a/.gitignore b/.gitignore
index fa601bce..ff8e5286 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,6 +20,5 @@ data/
 **/model.tar.gz
 **/*.safetensor
 **/*.json
-notes.md
-etc/
 .claude/tasks/
+.scratchpad/
diff --git a/.markdownlint.yaml b/.markdownlint.yaml
index a0e9ea32..414c5a86 100644
--- a/.markdownlint.yaml
+++ b/.markdownlint.yaml
@@ -15,6 +15,11 @@ MD033:
     - br
     - details
     - summary
+    # Custom XML-like tag used by Ralph workflow (maskfile.md) to signal task completion
     - promise
 # MD041 - First line in file should be top-level heading
 MD041: false
+# MD022 - Headings should be surrounded by blank lines
+MD022:
+  lines_below: 1
+  lines_above: 1