fix(cli): disambiguate reused flag names

[Kashkovsky]

Summary

• leave option spellings used as both boolean and valued flags unchanged for the selected Effect command parser
• fix init-manifest --replace before --repo and update --status before --json
• retain valued --replace and --status behavior in memory and projection commands

Tests

• focused Effect CLI integration regression
• bounded Fast-check non-mutation property, 100 runs
• CLI production-log unit tests, 9 passed
• source and test TypeScript checks
• focused oxlint and Prettier checks