fix: distinguish phase file writes from reads in PostToolUse hook

- Parse tool_name via jq: Write tool checks file_path match,
  Bash tool checks for redirect operator (>) with phase file path
- Reads (cat, head) no longer trigger false-positive markers
- Split guard into separate statements for clarity
- Move marker cleanup inside hook-install guard
- Expand tests: 5 cases covering Bash write, Write tool, Bash read,
  unrelated Bash, and Write to different file

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

lib/agent-session.sh

@@ -110,8 +110,8 @@ create_agent_session() {
           }
         }' > "$settings"
       fi
+      rm -f "$phase_marker"
     fi
-    rm -f "$phase_marker"
   fi
 
   rm -f "$idle_marker"

lib/hooks/on-phase-change.sh

@@ -2,9 +2,9 @@
 # on-phase-change.sh — PostToolUse hook for phase file write detection.
 #
 # Called by Claude Code after every Bash|Write tool execution.
-# Checks if the tool input references the phase file path and, if so,
-# writes a "phase-changed" timestamp marker so monitor_phase_loop can
-# react immediately instead of waiting for the next mtime-based poll.
+# Detects writes (not reads) to the phase file and writes a timestamp
+# marker so monitor_phase_loop can react immediately instead of waiting
+# for the next mtime-based poll.
 #
 # Usage (in .claude/settings.json):
 #   {"type": "command", "command": "this-script /path/to/phase-file /path/to/marker"}
@@ -14,11 +14,30 @@
 phase_file="${1:-}"
 marker_file="${2:-}"
 
+[ -z "$phase_file" ] && exit 0
+[ -z "$marker_file" ] && exit 0
+
 input=$(cat)  # consume hook JSON from stdin
 
-[ -z "$phase_file" ] || [ -z "$marker_file" ] && exit 0
+# Fast path: skip if phase file not referenced at all
+printf '%s' "$input" | grep -qF "$phase_file" || exit 0
 
-# Check if the tool input references the phase file path
-if printf '%s' "$input" | grep -qF "$phase_file"; then
-  date +%s > "$marker_file"
-fi
+# Parse tool type and detect writes only (ignore reads like cat/head)
+tool_name=$(printf '%s' "$input" | jq -r '.tool_name // empty' 2>/dev/null)
+
+case "$tool_name" in
+  Write)
+    # Write tool: check if file_path targets the phase file
+    file_path=$(printf '%s' "$input" | jq -r '.tool_input.file_path // empty' 2>/dev/null)
+    [ "$file_path" = "$phase_file" ] && date +%s > "$marker_file"
+    ;;
+  Bash)
+    # Bash tool: check if the decoded command contains a redirect (>)
+    # targeting the phase file — distinguishes writes from reads
+    command_str=$(printf '%s' "$input" | jq -r '.tool_input.command // empty' 2>/dev/null)
+    if printf '%s' "$command_str" | grep -qF "$phase_file" \
+       && printf '%s' "$command_str" | grep -q '>'; then
+      date +%s > "$marker_file"
+    fi
+    ;;
+esac