refactor(cloudflare): improve wrangler merge

[pi0]

Followup on #2949 and #3064 /cc @@petebacondarwin

This PR improves merging logic for generating wrangler.json:

• pages_build_output_dir, main and assets are always overridden + nitro shows warn when it does (this is because, relative paths in generated config are different than user ones
• nodejs_compat related flags are added with more care:
  • If user sets both nodejs_compat_v2 and no_nodejs_compat_v2, we warn + remove nodejs_compat_v2
  • If user sets only nodejs_compat_v2, we warn about incompatibility and avoid adding any defaults
  • otherwise we add nodejs_compat + no_nodejs_compat_v2