Fix: Respect excluded categories when manually marking chapters as read

[leodyversemilla07]

Fixes #1521

Problem

When manually marking chapters as read via menu, the 'delete after marked as read' feature incorrectly deletes chapters even in excluded categories. This happens because:

1. Stale data issue: Manual mark-as-read updates the database first, then checks exclusion filters using stale in-memory chapter objects that still have read=false
2. Exclusion logic: For excluded categories, the filter is: chapters.filterNot { it.read } (only delete unread chapters to protect read ones)
3. Result: With stale data showing read=false, the filter thinks the chapter is unread and includes it for deletion

Root Cause

The deletion logic in SetReadStatus.kt used in-memory chapter objects before they were refreshed from the database:

• Database gets updated: chapterRepository.update(readUpdate) ✅
• Deletion uses old in-memory objects: downloadManager.enqueueChaptersToDelete(chapters, manga) ❌
• These objects still have read=false even though database has read=true

Solution

Refresh chapter data from database before deletion to ensure exclusion filters see the updated read=true status:

// Fetch fresh data from database after marking as read
val updatedChapters = chapters.mapNotNull { chapter ->
    chapterRepository.getChapterById(chapter.id)
}

// Now deletion uses correct read status
downloadManager.enqueueChaptersToDelete(updatedChapters, manga)

Comparison with Automatic Mark-as-Read

Automatic (after reading in ReaderViewModel) - works correctly:

• Fetches fresh data: getChaptersByMangaId(manga.id) ✅
• Uses updated read status for deletion ✅

Manual (via menu) - was broken:

• Uses stale in-memory data ❌
• Bypasses exclusion filters ❌

This fix aligns manual behavior with the working automatic behavior.

Testing

• ✅ Manual mark as read now respects excluded categories
• ✅ Automatic mark as read continues to work as before
• ✅ Bookmarked chapter exclusion still works correctly

Technical Details

Files Modified:

• app/src/main/java/eu/kanade/domain/chapter/interactor/SetReadStatus.kt

Key Methods:

• DownloadManager.getChaptersToDelete() - contains exclusion filter
• DownloadManager.enqueueChaptersToDelete() - applies filters correctly
• ChapterRepository.getChapterById() - fetches fresh data

The exclusion filter protects chapters in excluded categories by only deleting unread ones. With fresh data showing read=true, these chapters are correctly excluded from deletion.