feat: sync scripts with agent + add 4 new scripts

scripts/git-identity-hook/git-identity-hook.sh

@@ -0,0 +1,66 @@
+#!/usr/bin/env bash
+# Soma — Git Identity Pre-Commit Hook
+#
+# Validates git user.email before allowing commits.
+# Two modes:
+#   1. If .soma/settings.json has guard.gitIdentity.email → enforces that exact email
+#   2. Otherwise → just checks that user.email is set (not empty)
+#
+# Note: this hook checks the first email value only. For multiple valid emails
+# (array format), the soma-guard.ts runtime check handles the full validation.
+# The hook is a lightweight safety net, not the primary enforcement.
+#
+# Install: copy to .git/hooks/pre-commit (or use `soma init --hooks`)
+# Or symlink: ln -sf ../../.soma/scripts/git-identity-hook.sh .git/hooks/pre-commit
+
+set -euo pipefail
+
+CURRENT_EMAIL=$(git config user.email 2>/dev/null || echo "")
+CURRENT_NAME=$(git config user.name 2>/dev/null || echo "")
+
+# --- Check if email is set at all ---
+if [ -z "$CURRENT_EMAIL" ]; then
+    echo "❌ git user.email is not set!"
+    echo ""
+    echo "Set it with:"
+    echo "  git config user.name \"Your Name\""
+    echo "  git config user.email \"you@example.com\""
+    echo ""
+    echo "Or add an includeIf to ~/.gitconfig for this directory."
+    exit 1
+fi
+
+# --- Check against .soma/settings.json if it exists ---
+SOMA_DIR=""
+# Walk up to find .soma/
+DIR="$(pwd)"
+while [ "$DIR" != "/" ]; do
+    if [ -d "$DIR/.soma" ]; then
+        SOMA_DIR="$DIR/.soma"
+        break
+    fi
+    DIR="$(dirname "$DIR")"
+done
+
+if [ -n "$SOMA_DIR" ] && [ -f "$SOMA_DIR/settings.json" ]; then
+    # Extract expected email (lightweight — no jq dependency)
+    EXPECTED_EMAIL=$(grep -o '"email"[[:space:]]*:[[:space:]]*"[^"]*"' "$SOMA_DIR/settings.json" 2>/dev/null | head -1 | sed 's/.*: *"\(.*\)"/\1/')
+
+    if [ -n "$EXPECTED_EMAIL" ] && [ "$CURRENT_EMAIL" != "$EXPECTED_EMAIL" ]; then
+        echo "⚠️  Git identity mismatch!"
+        echo ""
+        echo "  Current:  $CURRENT_NAME <$CURRENT_EMAIL>"
+        echo "  Expected: <$EXPECTED_EMAIL> (from .soma/settings.json)"
+        echo ""
+        echo "Fix with:"
+        echo "  git config user.email \"$EXPECTED_EMAIL\""
+        echo ""
+        echo "Or update .soma/settings.json guard.gitIdentity.email"
+        echo ""
+        echo "To commit anyway: git commit --no-verify"
+        exit 1
+    fi
+fi
+
+# Identity looks good
+exit 0

scripts/soma-code/soma-code.sh

@@ -33,10 +33,10 @@
 set -euo pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'
-  SOMA_GREEN='\033[0;32m'; SOMA_YELLOW='\033[0;33m'; SOMA_CYAN='\033[0;36m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"
+SOMA_GREEN="${SOMA_GREEN:-\033[0;32m}"; SOMA_YELLOW="${SOMA_YELLOW:-\033[0;33m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
 
 SHELL_DIR="${SOMA_SHELL_DIR:-$(pwd)}"
 RED='\033[0;31m'

scripts/soma-compat/soma-compat.sh

@@ -0,0 +1,235 @@
+#!/usr/bin/env bash
+# σ Soma Compatibility Check
+# Detects overlap, redundancy, and conflicting directives across protocols + muscles.
+# Usage: bash soma-compat.sh [path-to-soma-dir]
+set -o pipefail
+
+SOMA_DIR="${1:-$(pwd)/.soma}"
+[ ! -d "$SOMA_DIR" ] && SOMA_DIR="$(pwd)"
+
+PROTO_DIR="$SOMA_DIR/protocols"
+MUSCLE_DIR="$SOMA_DIR/memory/muscles"
+
+SCORE=100
+WARNINGS=0
+ISSUES=""
+
+# ── Helpers ──────────────────────────────────────────────────────
+
+extract_fm() {
+  awk '/^---$/{n++; next} n==1{print}' "$1"
+}
+
+extract_body() {
+  awk 'BEGIN{n=0} /^---$/{n++; next} n>=2{print}' "$1"
+}
+
+get_field() {
+  echo "$1" | grep -i "^$2:" | head -1 | sed "s/^$2: *//i" | tr -d '"' | tr -d "'" 
+}
+
+get_array() {
+  echo "$1" | grep -i "^$2:" | head -1 | sed "s/^$2: *//i" | tr -d '[]"'"'" | tr ',' '\n' | sed 's/^ *//;s/ *$//' | grep -v '^$'
+}
+
+get_name() {
+  local fm; fm=$(extract_fm "$1")
+  local name; name=$(get_field "$fm" "name")
+  [ -z "$name" ] && name=$(basename "$1" .md)
+  echo "$name"
+}
+
+warn() {
+  WARNINGS=$((WARNINGS + 1))
+  ISSUES="${ISSUES}\n  ⚠️  $1"
+  SCORE=$((SCORE - $2))
+}
+
+# ── Collect items ────────────────────────────────────────────────
+
+declare -a FILES=()
+declare -a NAMES=()
+declare -a TYPES=()
+declare -a TAG_SETS=()
+declare -a APPLIES_SETS=()
+declare -a DIRECTIVES=()
+
+idx=0
+for dir_info in "protocol:$PROTO_DIR" "muscle:$MUSCLE_DIR"; do
+  type="${dir_info%%:*}"
+  dir="${dir_info#*:}"
+  [ ! -d "$dir" ] && continue
+  for f in "$dir"/*.md; do
+    [ ! -f "$f" ] && continue
+    [[ "$(basename "$f")" == _* ]] && continue
+    [[ "$(basename "$f")" == "README.md" ]] && continue
+
+    fm=$(extract_fm "$f")
+    body=$(extract_body "$f")
+    name=$(get_field "$fm" "name")
+    [ -z "$name" ] && name=$(basename "$f" .md)
+
+    tags=$(get_array "$fm" "tags" | tr '\n' '|')
+    applies=$(get_array "$fm" "applies-to" | tr '\n' '|')
+    [ -z "$applies" ] && applies=$(get_array "$fm" "appliesTo" | tr '\n' '|')
+
+    # Extract directive words with context
+    directives=$(echo "$body" | grep -oiE "(always|never|must|don.t|stop|avoid|require|forbid|prohibited)[^.!]*[.!]" | head -20 | tr '\n' '|')
+
+    FILES[$idx]="$f"
+    NAMES[$idx]="$name"
+    TYPES[$idx]="$type"
+    TAG_SETS[$idx]="$tags"
+    APPLIES_SETS[$idx]="$applies"
+    DIRECTIVES[$idx]="$directives"
+    idx=$((idx + 1))
+  done
+done
+
+TOTAL=$idx
+
+if [ "$TOTAL" -lt 2 ]; then
+  echo "σ Compatibility Check — $TOTAL items (need 2+ to compare)"
+  exit 0
+fi
+
+# ── Compare pairs ────────────────────────────────────────────────
+
+tag_overlap() {
+  local a="$1" b="$2"
+  local shared=0 total_a=0 total_b=0
+
+  IFS='|' read -ra A <<< "$a"
+  IFS='|' read -ra B <<< "$b"
+  total_a=${#A[@]}
+  total_b=${#B[@]}
+
+  for ta in "${A[@]}"; do
+    [ -z "$ta" ] && continue
+    for tb in "${B[@]}"; do
+      [ -z "$tb" ] && continue
+      [ "$ta" = "$tb" ] && shared=$((shared + 1))
+    done
+  done
+
+  local max=$total_a
+  [ $total_b -gt $max ] && max=$total_b
+  [ $max -eq 0 ] && echo 0 && return
+  echo $((shared * 100 / max))
+}
+
+directive_conflicts() {
+  local a="$1" b="$2"
+  local conflicts=""
+
+  # Check for always/never on same topic
+  IFS='|' read -ra DA <<< "$a"
+  IFS='|' read -ra DB <<< "$b"
+
+  for da in "${DA[@]}"; do
+    [ -z "$da" ] && continue
+    da_lower=$(echo "$da" | tr '[:upper:]' '[:lower:]')
+    for db in "${DB[@]}"; do
+      [ -z "$db" ] && continue
+      db_lower=$(echo "$db" | tr '[:upper:]' '[:lower:]')
+
+      # "always X" vs "never X" or "don't X" 
+      if echo "$da_lower" | grep -q "^always" && echo "$db_lower" | grep -q "^never\|^don.t\|^stop\|^avoid"; then
+        # Check if they share a key noun (3+ char words)
+        for word in $(echo "$da_lower" | tr -cs '[:alpha:]' '\n' | awk 'length>=4'); do
+          if echo "$db_lower" | grep -qi "$word"; then
+            conflicts="${conflicts}CONFLICT: \"${da:0:60}\" vs \"${db:0:60}\"\n"
+            break
+          fi
+        done
+      fi
+      # Reverse
+      if echo "$db_lower" | grep -q "^always" && echo "$da_lower" | grep -q "^never\|^don.t\|^stop\|^avoid"; then
+        for word in $(echo "$db_lower" | tr -cs '[:alpha:]' '\n' | awk 'length>=4'); do
+          if echo "$da_lower" | grep -qi "$word"; then
+            conflicts="${conflicts}CONFLICT: \"${db:0:60}\" vs \"${da:0:60}\"\n"
+            break
+          fi
+        done
+      fi
+    done
+  done
+
+  echo -e "$conflicts"
+}
+
+scope_overlap() {
+  local a="$1" b="$2"
+  [ -z "$a" ] || [ -z "$b" ] && echo 0 && return
+  [ "$a" = "|" ] || [ "$b" = "|" ] && echo 0 && return
+
+  # "always" applies to everything — high overlap with anything
+  if echo "$a" | grep -q "always" && echo "$b" | grep -q "always"; then
+    echo 50
+    return
+  fi
+
+  tag_overlap "$a" "$b"
+}
+
+# ── Run comparisons ─────────────────────────────────────────────
+
+for ((i=0; i<TOTAL; i++)); do
+  for ((j=i+1; j<TOTAL; j++)); do
+    name_a="${NAMES[$i]}"
+    name_b="${NAMES[$j]}"
+
+    # Tag overlap
+    toverlap=$(tag_overlap "${TAG_SETS[$i]}" "${TAG_SETS[$j]}")
+
+    # Scope overlap
+    soverlap=$(scope_overlap "${APPLIES_SETS[$i]}" "${APPLIES_SETS[$j]}")
+
+    # Directive conflicts
+    dconflicts=$(directive_conflicts "${DIRECTIVES[$i]}" "${DIRECTIVES[$j]}")
+
+    # High tag overlap = redundancy warning
+    if [ "$toverlap" -ge 70 ]; then
+      warn "REDUNDANCY: $name_a ↔ $name_b — ${toverlap}% tag overlap" 3
+    elif [ "$toverlap" -ge 50 ]; then
+      warn "OVERLAP: $name_a ↔ $name_b — ${toverlap}% tag overlap" 1
+    fi
+
+    # Directive conflicts
+    if [ -n "$dconflicts" ]; then
+      count=$(echo -e "$dconflicts" | grep -c "CONFLICT" || true)
+      warn "DIRECTIVE CONFLICT: $name_a ↔ $name_b ($count conflicts)" 5
+      while IFS= read -r line; do
+        [ -n "$line" ] && ISSUES="${ISSUES}\n     $line"
+      done <<< "$(echo -e "$dconflicts" | grep "CONFLICT")"
+    fi
+  done
+done
+
+# ── Output ───────────────────────────────────────────────────────
+
+[ $SCORE -lt 0 ] && SCORE=0
+
+echo ""
+echo "σ Compatibility Check — $TOTAL items ($( echo "${TYPES[@]}" | tr ' ' '\n' | grep -c protocol || true) protocols, $( echo "${TYPES[@]}" | tr ' ' '\n' | grep -c muscle || true) muscles)"
+echo "═══════════════════════════════════════"
+
+if [ $SCORE -ge 90 ]; then
+  echo "  ✅ $SCORE/100 — highly compatible"
+elif [ $SCORE -ge 70 ]; then
+  echo "  ⚠️  $SCORE/100 — some overlap detected"
+elif [ $SCORE -ge 50 ]; then
+  echo "  🟡 $SCORE/100 — review recommended"
+else
+  echo "  🔴 $SCORE/100 — significant conflicts"
+fi
+
+if [ -n "$ISSUES" ]; then
+  echo -e "$ISSUES"
+fi
+
+echo "═══════════════════════════════════════"
+
+[ $WARNINGS -gt 5 ] && exit 2
+[ $WARNINGS -gt 0 ] && exit 1
+exit 0

scripts/soma-focus/soma-focus.sh

@@ -21,9 +21,9 @@
 set -eo pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'; SOMA_CYAN='\033[0;36m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
 # ── Project root discovery ──
 find_project_root() {
   local dir="$PWD"

scripts/soma-plans/soma-plans.sh

@@ -23,9 +23,9 @@
 set -euo pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'; SOMA_CYAN='\033[0;36m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
 SOMA_DIR=""
 for d in .soma "$HOME/.soma"; do
   [[ -d "$d" ]] && SOMA_DIR="$d" && break

scripts/soma-query/soma-query.sh

@@ -37,9 +37,9 @@
 set -uo pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'; SOMA_CYAN='\033[0;36m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
 # ── Paths ────────────────────────────────────────────────────────────────
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"

scripts/soma-reflect/soma-reflect.sh

@@ -41,10 +41,10 @@
 set -uo pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'; SOMA_CYAN='\033[0;36m'
-  SOMA_GREEN='\033[0;32m'; SOMA_RED='\033[0;31m'; SOMA_YELLOW='\033[0;33m'; SOMA_MAGENTA='\033[0;35m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
+SOMA_GREEN="${SOMA_GREEN:-\033[0;32m}"; SOMA_RED="${SOMA_RED:-\033[0;31m}"; SOMA_YELLOW="${SOMA_YELLOW:-\033[0;33m}"; SOMA_MAGENTA="${SOMA_MAGENTA:-\033[0;35m}"
 BOLD="${SOMA_BOLD:-\033[1m}"
 DIM="${SOMA_DIM:-\033[2m}"
 NC="${SOMA_NC:-\033[0m}"

scripts/soma-scrape/soma-scrape.sh

@@ -39,9 +39,9 @@
 set -o pipefail
 
 # ── Theme ──
-source "$(dirname "$0")/soma-theme.sh" 2>/dev/null || {
-  SOMA_BOLD='\033[1m'; SOMA_DIM='\033[2m'; SOMA_NC='\033[0m'; SOMA_CYAN='\033[0;36m'
-}
+_sd="$(dirname "$0")"
+if [ -f "$_sd/soma-theme.sh" ]; then source "$_sd/soma-theme.sh"; fi
+SOMA_BOLD="${SOMA_BOLD:-\033[1m}"; SOMA_DIM="${SOMA_DIM:-\033[2m}"; SOMA_NC="${SOMA_NC:-\033[0m}"; SOMA_CYAN="${SOMA_CYAN:-\033[0;36m}"
 # ── Configurable Variables ──────────────────────────────────────────────────
 
 # Where scraped docs live