Improve papis workflow with enhanced functions and aliases

- Convert pafile and pafinder aliases to shell functions with better parameter handling
- Make pafile query parameter optional for interactive document selection
- Add patag function for hash-separated multi-tag addition (e.g., patag "tag1#tag2" query)
- Add paopen alias for quick document opening
- Update README to document all papis workflow shortcuts and functions
- Fix deprecated zsh initExtra to initContent

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

README.md

@@ -460,21 +460,31 @@ papis export --format bibtex query_term > references.bib
 papis list --format '{doc[author]} - {doc[title]} ({doc[year]})'
 ```
 
-**Workflow Aliases:**
+**Workflow Aliases and Functions:**
 ```bash
 # Bibliography formatting
 pals                          # List documents with formatted template
 pals "machine learning"       # Search and format specific documents
 
-# File operations  
+# File operations (shell functions)
-pafile filename.pdf [query]   # Add file from ~/Downloads/ to existing entry
+pafile filename.pdf           # Add file from ~/Downloads/ (interactive selection)
+pafile filename.pdf "query"   # Add file from ~/Downloads/ to matching entry
+pafile /path/to/file.pdf      # Add file using absolute path
 paurl [url] [query]           # Add file from URL to existing entry
 
+# Document access
+paopen                        # Open documents interactively
+paopen "query"                # Open documents matching query
+
 # Directory access (shell function)
 pafinder                      # Open first document directory in Finder
 pafinder "query"              # Open first matching document directory
 pafinder author:einstein      # Open first Einstein paper directory
 pafinder --sort year smith    # Open newest Smith paper directory
+
+# Tagging (shell function)
+patag "tag1#tag2" "query"     # Add multiple tags using # separator
+patag "materials#ai4science" amorphous  # Example: add two tags to matching docs
 ```
 
 **Configuration location**: `modules/papis.nix` with embedded configuration

modules/papis.nix

@@ -102,5 +102,32 @@
         fi
       fi
     }
+    
+    # Papis tag function - add multiple tags using hash-separated format
+    patag() {
+      if [ $# -ne 2 ]; then
+        echo "Usage: patag \"tag1#tag2#tag3\" <query>"
+        echo "Example: patag \"materials#ai4science\" amorphous"
+        echo "Example: patag \"quantum#computing\" \"author:einstein\""
+        return 1
+      fi
+      
+      local tags_string="$1"
+      local query="$2"
+      
+      # Split tags by # and build --add arguments
+      local add_args=""
+      IFS='#' read -ra tags <<< "$tags_string"
+      for tag in "${tags[@]}"; do
+        # Trim whitespace and add to arguments
+        tag=$(echo "$tag" | xargs)
+        if [ -n "$tag" ]; then
+          add_args="$add_args --add \"$tag\""
+        fi
+      done
+      
+      # Execute the papis tag command
+      eval "papis tag $add_args \"$query\""
+    }
   '';
 }