refactor(download): mark episode downloaded instead of deleting

Change _remove_episode_from_missing_list to set is_downloaded=True
and populate file_path via EpisodeService.mark_downloaded, instead of
deleting the Episode row. Preserves download history so queries can
distinguish series with downloaded episodes from completely unwatched
series.

- Pass serie_folder to construct file_path
- Look up series_id via AnimeSeriesService.get_by_key
- Update tests to mock mark_downloaded path
- Document episode lifecycle in docs/DEVELOPMENT.md

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

docs/DEVELOPMENT.md

@@ -82,6 +82,22 @@ The download queue prevents duplicate entries at two levels:
 - 5-minute cooldown prevents rapid re-triggers
 - Checked at start of `_auto_download_missing()`
 
+### Episode Lifecycle
+
+Episodes transition through states stored in the `episodes` table:
+
+| State | `is_downloaded` | `file_path` | Description |
+|-------|----------------|-------------|-------------|
+| Missing | `False` | `NULL` | Episode not yet downloaded |
+| Downloaded | `True` | Set | Episode exists on disk |
+
+**State Transitions:**
+1. **Missing → Downloaded**: When download completes, `_remove_episode_from_missing_list()` calls `EpisodeService.mark_downloaded()` to set `is_downloaded=True` and populate `file_path`. The episode record is NOT deleted.
+
+**Query Implications:**
+- `get_series_with_missing_episodes()`: Filters for `is_downloaded=False` to find series with undownloaded episodes
+- `get_series_with_no_episodes()`: Finds series with `is_downloaded=False` episodes but NO `is_downloaded=True` episodes (completely unwatched series)
+
 ### Mocking the Download Queue
 
 When testing components that use the download queue: