SET command only works in REPL mode, not via -c flag

## Description
`SET format = side` and similar SET commands produce parse errors when used with `-c` flag or piped input.

## Steps to Reproduce
```
./mxcli -p project.mpr -c "set format = side"
```

## Expected
Format setting applied

## Actual
Parse error

## Severity
Low

## Test Case Reference
session-test-cases.md §5.1–§5.3