fix: JSON and directory handling

[mdqst]

Description

I’ve improved the scripts to handle JSON and directory checks more reliably:

• while read loops now run in the current process using process substitution, so file updates work correctly.
• added checks for missing directories in tsconfig.json to prevent errors.
• version checks now handle empty or null values from package.json properly.
• removed the -r flag when modifying JSON with jq to preserve the correct structure.

these changes ensure the scripts run smoothly without failing on missing paths or malformed JSON.

Type of change

• Bug fix (non-breaking change which fixes an issue)

Checklist

• I have tested locally
• I have performed a self review of my changes
• My code is up to date with the base branch

[stwiname]

This script doesn't work. When i try to build a docker image it fails. docker build . -f ./packages/node/Dockerfile -t subquerynetwork/subql-node:local