[RR] Fix discover logic

[lynzrand]

Fix discover accidentally descending into another module.

Closes #1095. Atop #1096

[semanticdiff-com]

Review changes with  

Changed Files

File	Status
crates/moonbuild-rupes-recta/src/discover.rs	90% smaller

[peter-jerry-ye-code-review]

Critical bug fix: reordered checks to prevent descending into other modules

Category
Correctness
Code Snippet
Lines 143-164 in discover.rs: Moved the module check before the package check
Recommendation
The current implementation is correct. The module check should happen before the package check to prevent accidentally discovering packages in other modules.
Reasoning
This fixes the core issue described in the PR. By checking for MOON_MOD_JSON before MOON_PKG_JSON, the discovery process correctly avoids descending into other modules, which was the root cause of issue #1095.

Deprecated flag properly marked with warning and hidden from help

Category
Maintainability
Code Snippet
Lines 57-59 and 77-79 in info.rs: Added deprecation comment and warning
Recommendation
Consider setting a specific timeline for removal and adding it to the warning message, e.g., 'will be removed in version X.Y'
Reasoning
The deprecation is handled well with both hiding the flag from help and warning users, but a specific removal timeline would help users plan migration better.

Documentation updated to reflect deprecated flag removal

Category
Maintainability
Code Snippet
Lines 321 in commands.md: Removed --no-alias from documentation
Recommendation
Current implementation is good - removing deprecated options from documentation prevents new users from adopting deprecated features.
Reasoning
Consistent with the deprecation strategy, removing the flag from documentation while keeping the warning for existing users is the right approach.