Add this as a "Run Script" build phase in Xcode to enable Charles Proxy on iOS 9

enable-charles-proxy.sh

#!/bin/sh

#  enable-charles-proxy.sh
#
#  Created by John Boiles on 9/21/15.
#
#  This script sets :NSAppTransportSecurity:NSAllowsArbitraryLoads to true in the Info.plist file if building the Debug configuration.
#  This enables debugging from https proxies such as Charles.

INFO_PLIST="${TARGET_BUILD_DIR}/${INFOPLIST_PATH}"
PLISTBUDDY="/usr/libexec/PlistBuddy"

if [ "${CONFIGURATION}" == "Debug" ]; then
    $PLISTBUDDY -c "Add :NSAppTransportSecurity dict" "${INFO_PLIST}" || true
    $PLISTBUDDY -c "Add :NSAppTransportSecurity:NSAllowsArbitraryLoads bool true" "${INFO_PLIST}" || true
    $PLISTBUDDY -c "Set :NSAppTransportSecurity:NSAllowsArbitraryLoads true" "${INFO_PLIST}"
else
    $PLISTBUDDY -c "Delete :NSAppTransportSecurity:NSAllowsArbitraryLoads" "${INFO_PLIST}" || true
fi

ALLOWS_ARBITRARY_LOADS_ENABLED=$($PLISTBUDDY -c "Print :NSAppTransportSecurity:NSAllowsArbitraryLoads" "${INFO_PLIST}")
if [ "${ALLOWS_ARBITRARY_LOADS_ENABLED}" == "true" ]; then
    echo "Warning: :NSAppTransportSecurity:NSAllowsArbitraryLoads set to true (potentially insecure)."
fi

If you want this script to work consistently remember to specify in the input files the following $(TARGET_BUILD_DIR)/$(INFOPLIST_PATH). This ensures things happen in the correct order.

I was experiencing a problem where it would work on clean build but all incremental builds would fail due to the plist file change being overridden by the original plist file.