fix: resolve lines.indexOf bug and safe string replacement pattern bugs in scripts

[MatrixNeoKozak]

This change fixes two critical bugs in the project's helper scripts:

1. In scripts/check-skills-index.mjs, the method parseSkillsIndex previously utilized lines.indexOf(line) to obtain the line number of the skill entry in the skills-index.yaml file. If there were identical lines in the file (such as identical formatting, sections, or comments), indexOf would yield the index of the first occurrence instead of the active loop index. This is resolved by iterating over lines using a standard index-based loop and computing the line number directly from the loop variable index.

2. In scripts/sync-plugins.mjs, the method injectDeprecationNotice used string replacement with dynamic arguments (notice, currentDesc, and newFm). Because JS String.prototype.replace treats $ as a special replacement pattern prefix (e.g., matching $& to duplicate the match), any occurrence of $ in the description or deprecation notice would be improperly parsed and expand to arbitrary matched substrings. This is corrected by supplying replacement callback functions to the replace calls, preventing pattern expansion bugs.

[shinpr]

Thanks for the fix. Both look correct, merging.