Fixing FilePad.update_file()

[yeyuan98]

Note: This bug fix was created with help of coding agents. Would greatly appreciate any feedback & happy to make further changes.

Summary

FilePad.update_file() and FilePad.update_file_by_id() are broken on main, causing the following problems:

• updates are silently lost
• GridFS storage leaks

This PR includes fixes and documentation updates to correct bugs in the file update feature of FilePad.

Issue list

#	Bug	Impact
1	_update_file_contents() never calls update_one() to persist the new gfs_id to MongoDB	File updates are silently lost — get_file() always returns old content
2	from_db_file() passes database= to __init__(), but the parameter is named name	Instant TypeError — from_db_file() is unusable
3	_update_file_contents() deletes old GridFS entry before writing the new one	If the new file write fails, the old data is permanently lost
4	gridfs.delete() called with string gfs_id instead of ObjectId	Silent no-op — GridFS entries are never cleaned up, causing storage leaks
5	zlib.compress(contents, compress) passes boolean True as compression level	Compresses at level 1 (weakest) instead of default level 6 — storage inefficiency
6	open(path, read_mode).read() in _update_file_contents never closes the file handle	File handle leak on every update

Fix list

fireworks/utilities/filepad.py (lines 257, 304, 334–342, 375):

• Line 257 (delete_file_by_id): Wrap gfs_id with ObjectId() for proper GridFS deletion.
• Line 304 (_insert_to_gridfs): Remove boolean compress argument from zlib.compress() call, using the default level 6.
• Lines 334–342 (_update_file_contents): Three fixes applied together:
  • Use with open() context manager to prevent file handle leak.
  • Reorder: insert new GridFS entry first, then delete old one (prevents data loss on failure).
  • Add missing self.filepad.update_one() call to persist the new gfs_id and compressed flag to MongoDB.
• Line 375 (from_db_file): Rename database= keyword argument to name= to match __init__ signature.

fireworks/utilities/tests/test_filepad.py:

• Import ObjectId for proper GridFS existence checks.
• test_update_file: Add round-trip assertion — after update, verify get_file() returns updated content and gfs_id matches.
• test_update_file_by_id: Add round-trip assertion — after update, verify get_file_by_id() returns correct content and metadata.

This fix also contains docstring and package doc changes relevant to FilePad's file update functionality.