Merge branch 'master' into docs-migrate-25-10-plugin-registry

Author: bentsherman

.github/workflows/seqeradocs-changelog.yml

@@ -75,7 +75,7 @@ EOF
 done
 
 # Source common functions
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths and validate branch

.specify/scripts/bash/check-prerequisites.sh

@@ -7,7 +7,7 @@ get_repo_root() {
         git rev-parse --show-toplevel
     else
         # Fall back to script location for non-git repos
-        local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+        local script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
         (cd "$script_dir/../../.." && pwd)
     fi
 }
@@ -37,7 +37,7 @@ get_current_branch() {
         for dir in "$specs_dir"/*; do
             if [[ -d "$dir" ]]; then
                 local dirname=$(basename "$dir")
-                if [[ "$dirname" =~ ^([0-9]{3})- ]]; then
+                if [[ "$dirname" =~ ^([0-9]{6})- ]]; then
                     local number=${BASH_REMATCH[1]}
                     number=$((10#$number))
                     if [[ "$number" -gt "$highest" ]]; then
@@ -72,9 +72,10 @@ check_feature_branch() {
         return 0
     fi
 
-    if [[ ! "$branch" =~ ^[0-9]{3}- ]]; then
+    # Accept date-based format (YYMMDD-feature)
+    if [[ ! "$branch" =~ ^[0-9]{6}- ]]; then
         echo "ERROR: Not on a feature branch. Current branch: $branch" >&2
-        echo "Feature branches should be named like: 001-feature-name" >&2
+        echo "Feature branches should be named like: YYMMDD-feature-name (e.g., 251030-nextflow-modules)" >&2
         return 1
     fi
 
@@ -84,14 +85,14 @@ check_feature_branch() {
 get_feature_dir() { echo "$1/specs/$2"; }
 
 # Find feature directory by numeric prefix instead of exact branch match
-# This allows multiple branches to work on the same spec (e.g., 004-fix-bug, 004-add-feature)
+# This allows multiple branches to work on the same spec (e.g., 251030-fix-bug, 251030-add-feature)
 find_feature_dir_by_prefix() {
     local repo_root="$1"
     local branch_name="$2"
     local specs_dir="$repo_root/specs"
 
-    # Extract numeric prefix from branch (e.g., "004" from "004-whatever")
-    if [[ ! "$branch_name" =~ ^([0-9]{3})- ]]; then
+    # Extract numeric prefix from branch (e.g., "251030" from "251030-whatever")
+    if [[ ! "$branch_name" =~ ^([0-9]{6})- ]]; then
         # If branch doesn't have numeric prefix, fall back to exact match
         echo "$specs_dir/$branch_name"
         return

.specify/scripts/bash/common.sh

@@ -4,7 +4,6 @@ set -e
 
 JSON_MODE=false
 SHORT_NAME=""
-BRANCH_NUMBER=""
 ARGS=()
 i=1
 while [ $i -le $# ]; do
@@ -27,31 +26,22 @@ while [ $i -le $# ]; do
             fi
             SHORT_NAME="$next_arg"
             ;;
-        --number)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            BRANCH_NUMBER="$next_arg"
-            ;;
-        --help|-h) 
-            echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>"
+        --help|-h)
+            echo "Usage: $0 [--json] [--short-name <name>] <feature_description>"
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
             echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
-            echo "  --number N          Specify branch number manually (overrides auto-detection)"
             echo "  --help, -h          Show this help message"
             echo ""
+            echo "Branch naming: Uses YYMMDD-<feature-name> format (e.g., 251023-user-auth)"
+            echo ""
             echo "Examples:"
             echo "  $0 'Add user authentication system' --short-name 'user-auth'"
-            echo "  $0 'Implement OAuth2 integration for API' --number 5"
+            echo "  # Creates: 251023-user-auth (if run on Oct 23, 2025)"
+            echo ""
+            echo "  $0 'Implement OAuth2 integration for API'"
+            echo "  # Creates: 251023-oauth2-integration-api"
             exit 0
             ;;
         *) 
@@ -63,7 +53,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] <feature_description>" >&2
     exit 1
 fi
 
@@ -80,94 +70,10 @@ find_repo_root() {
     return 1
 }
 
-# Function to get highest number from specs directory
-get_highest_from_specs() {
-    local specs_dir="$1"
-    local highest=0
-    
-    if [ -d "$specs_dir" ]; then
-        for dir in "$specs_dir"/*; do
-            [ -d "$dir" ] || continue
-            dirname=$(basename "$dir")
-            number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
-            number=$((10#$number))
-            if [ "$number" -gt "$highest" ]; then
-                highest=$number
-            fi
-        done
-    fi
-    
-    echo "$highest"
-}
-
-# Function to get highest number from git branches
-get_highest_from_branches() {
-    local highest=0
-    
-    # Get all branches (local and remote)
-    branches=$(git branch -a 2>/dev/null || echo "")
-    
-    if [ -n "$branches" ]; then
-        while IFS= read -r branch; do
-            # Clean branch name: remove leading markers and remote prefixes
-            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
-            
-            # Extract feature number if branch matches pattern ###-*
-            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
-                number=$((10#$number))
-                if [ "$number" -gt "$highest" ]; then
-                    highest=$number
-                fi
-            fi
-        done <<< "$branches"
-    fi
-    
-    echo "$highest"
-}
-
-# Function to check existing branches (local and remote) and return next available number
-check_existing_branches() {
-    local short_name="$1"
-    local specs_dir="$2"
-    
-    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    git fetch --all --prune 2>/dev/null || true
-    
-    # Find all branches matching the pattern using git ls-remote (more reliable)
-    local remote_branches=$(git ls-remote --heads origin 2>/dev/null | grep -E "refs/heads/[0-9]+-${short_name}$" | sed 's/.*\/\([0-9]*\)-.*/\1/' | sort -n)
-    
-    # Also check local branches
-    local local_branches=$(git branch 2>/dev/null | grep -E "^[* ]*[0-9]+-${short_name}$" | sed 's/^[* ]*//' | sed 's/-.*//' | sort -n)
-    
-    # Check specs directory as well
-    local spec_dirs=""
-    if [ -d "$specs_dir" ]; then
-        spec_dirs=$(find "$specs_dir" -maxdepth 1 -type d -name "[0-9]*-${short_name}" 2>/dev/null | xargs -n1 basename 2>/dev/null | sed 's/-.*//' | sort -n)
-    fi
-    
-    # Combine all sources and get the highest number
-    local max_num=0
-    for num in $remote_branches $local_branches $spec_dirs; do
-        if [ "$num" -gt "$max_num" ]; then
-            max_num=$num
-        fi
-    done
-    
-    # Return next number
-    echo $((max_num + 1))
-}
-
-# Function to clean and format a branch name
-clean_branch_name() {
-    local name="$1"
-    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
-}
-
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 if git rev-parse --show-toplevel >/dev/null 2>&1; then
     REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -186,6 +92,9 @@ cd "$REPO_ROOT"
 SPECS_DIR="$REPO_ROOT/specs"
 mkdir -p "$SPECS_DIR"
 
+# Use YYMMDD format for feature numbering (date-based prefix)
+FEATURE_NUM=$(date +%y%m%d)
+
 # Function to generate branch name with stop word filtering and length filtering
 generate_branch_name() {
     local description="$1"
@@ -229,33 +138,19 @@ generate_branch_name() {
         echo "$result"
     else
         # Fallback to original logic if no meaningful words found
-        local cleaned=$(clean_branch_name "$description")
-        echo "$cleaned" | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
+        echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//' | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
     fi
 }
 
 # Generate branch name
 if [ -n "$SHORT_NAME" ]; then
     # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
+    BRANCH_SUFFIX=$(echo "$SHORT_NAME" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//')
 else
     # Generate from description with smart filtering
     BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
 fi
 
-# Determine branch number
-if [ -z "$BRANCH_NUMBER" ]; then
-    if [ "$HAS_GIT" = true ]; then
-        # Check existing branches on remotes
-        BRANCH_NUMBER=$(check_existing_branches "$BRANCH_SUFFIX" "$SPECS_DIR")
-    else
-        # Fall back to local directory check
-        HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-        BRANCH_NUMBER=$((HIGHEST + 1))
-    fi
-fi
-
-FEATURE_NUM=$(printf "%03d" "$BRANCH_NUMBER")
 BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
 
 # GitHub enforces a 244-byte limit on branch names

.specify/scripts/bash/create-new-feature.sh

@@ -24,7 +24,7 @@ for arg in "$@"; do
 done
 
 # Get script directory and load common functions
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions