<commit_before># Changelog
All notable changes to this project will be documented in this file.
This project **does not** adhere to [Semantic Versioning](http://semver.org/).
This file tries to follow the conventions proposed by [keepachangelog.com](http://keepachangelog.com/).
Here, the categories "Changed" for added and changed functionality,
"Fixed" for fixed functionality, and
"Removed" for removed functionality is used.

We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`,
to [sourceforge bugs](https://sourceforge.net/p/jabref/bugs/) by using `bug NUM`, and
to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by using `feature request NUM`.

## [Unreleased]

### Changed
- Implemented [#756](https://github.com/JabRef/jabref/issues/756): Add possibility to reformat all entries on save (under Preferences, File)
- Comments and preamble are serialized with capitalized first letter, i.e. `@Comment` instead of `@comment` and `@Preamble` instead of `@PREAMBLE`.
- Global sorting options and preferences are removed. Databases can still be sorted on save, but this is configured locally and stored in the file
- OvidImporter now also imports fields: doi, issn, language and keywords
- Implemented [#647](https://github.com/JabRef/jabref/issues/647): The preview can now be copied
- [#459](https://github.com/JabRef/jabref/issues/459) Open default directory when trying to add files to an entry
- Implemented [#668](https://github.com/JabRef/jabref/issues/668): Replace clear with icon to reduce search bar width
- Improved layout for OSX: Toolbar buttons and search field
- Migrated JabRef help to markdown at https://github.com/JabRef/help.jabref.org
- BibTeX and BibLaTeX mode is now file based and can be switched at runtime. The information is stored in the .bib file, and if it is not there detected by the entry types.
- Moved all quality-related database actions inside a new quality menu
- [#684](https://github.com/JabRef/jabref/issues/684): ISBNtoBibTex Error Message is now more clear 


### Fixed
- Fixed [#621](https://github.com/JabRef/jabref/issues/621) and [#669](https://github.com/JabRef/jabref/issues/669): Encoding and preamble now end with newline.
- Make BibTex parser more robust against missing newlines
- Fix bug that prevented the import of BibTex entries having only a key as content
- Fixed [#666](https://github.com/JabRef/jabref/issues/666): MS Office 2007 export is working again
- Fixed [#670](https://github.com/JabRef/jabref/issues/670): Expressions using enclosed quotes (keywords="one two") did not work.
- Fixed [#667](https://github.com/JabRef/jabref/issues/667): URL field is not sanitized anymore upon opening in browser.
- Fixed [#687](https://github.com/JabRef/jabref/issues/687): Fixed NPE when closing JabRef with new unsaved database.
- Fixed [#680](https://github.com/JabRef/jabref/issues/680): Synchronize Files key binding works again.
- Fixed [#212](https://github.com/JabRef/jabref/issues/212): Added command line option -g for autogenerating bibtex keys
- Fixed [#213](https://github.com/JabRef/jabref/issues/212): Added command line option -asfl for autosetting file links
- Fixed [#671](https://github.com/JabRef/jabref/issues/671): Remember working directory of last import
- IEEEXplore fetcher replaces keyword separator with the preferred
- Fixed [#710](https://github.com/JabRef/jabref/issues/710): Fixed quit behaviour under OSX
- Merge from DOI now honors removed fields
- Fixed [#778](https://github.com/JabRef/jabref/issues/778): Fixed NPE when exporting to .sql File


### Removed
- Fixed [#627](https://github.com/JabRef/jabref/issues/627): The pdf field is removed from the export formats, use the file field
- Removed configuration option to use database file directory as base directory for attached files and make it default instead.<commit_msg>Resolves #789 Preference for default file-based mode<commit_after># Changelog
All notable changes to this project will be documented in this file.
This project **does not** adhere to [Semantic Versioning](http://semver.org/).
This file tries to follow the conventions proposed by [keepachangelog.com](http://keepachangelog.com/).
Here, the categories "Changed" for added and changed functionality,
"Fixed" for fixed functionality, and
"Removed" for removed functionality is used.

We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`,
to [sourceforge bugs](https://sourceforge.net/p/jabref/bugs/) by using `bug NUM`, and
to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by using `feature request NUM`.

## [Unreleased]

### Changed
- Implemented [#756](https://github.com/JabRef/jabref/issues/756): Add possibility to reformat all entries on save (under Preferences, File)
- Comments and preamble are serialized with capitalized first letter, i.e. `@Comment` instead of `@comment` and `@Preamble` instead of `@PREAMBLE`.
- Global sorting options and preferences are removed. Databases can still be sorted on save, but this is configured locally and stored in the file
- OvidImporter now also imports fields: doi, issn, language and keywords
- Implemented [#647](https://github.com/JabRef/jabref/issues/647): The preview can now be copied
- [#459](https://github.com/JabRef/jabref/issues/459) Open default directory when trying to add files to an entry
- Implemented [#668](https://github.com/JabRef/jabref/issues/668): Replace clear with icon to reduce search bar width
- Improved layout for OSX: Toolbar buttons and search field
- Migrated JabRef help to markdown at https://github.com/JabRef/help.jabref.org
- BibTeX and BibLaTeX mode is now file based and can be switched at runtime. The information is stored in the .bib file, and if it is not there detected by the entry types.
- Moved all quality-related database actions inside a new quality menu
- [#684](https://github.com/JabRef/jabref/issues/684): ISBNtoBibTex Error Message is now more clear
- Moved default TeX mode to general preferences tab


### Fixed
- Fixed [#621](https://github.com/JabRef/jabref/issues/621) and [#669](https://github.com/JabRef/jabref/issues/669): Encoding and preamble now end with newline.
- Make BibTex parser more robust against missing newlines
- Fix bug that prevented the import of BibTex entries having only a key as content
- Fixed [#666](https://github.com/JabRef/jabref/issues/666): MS Office 2007 export is working again
- Fixed [#670](https://github.com/JabRef/jabref/issues/670): Expressions using enclosed quotes (keywords="one two") did not work.
- Fixed [#667](https://github.com/JabRef/jabref/issues/667): URL field is not sanitized anymore upon opening in browser.
- Fixed [#687](https://github.com/JabRef/jabref/issues/687): Fixed NPE when closing JabRef with new unsaved database.
- Fixed [#680](https://github.com/JabRef/jabref/issues/680): Synchronize Files key binding works again.
- Fixed [#212](https://github.com/JabRef/jabref/issues/212): Added command line option -g for autogenerating bibtex keys
- Fixed [#213](https://github.com/JabRef/jabref/issues/212): Added command line option -asfl for autosetting file links
- Fixed [#671](https://github.com/JabRef/jabref/issues/671): Remember working directory of last import
- IEEEXplore fetcher replaces keyword separator with the preferred
- Fixed [#710](https://github.com/JabRef/jabref/issues/710): Fixed quit behaviour under OSX
- Merge from DOI now honors removed fields
- Fixed [#778](https://github.com/JabRef/jabref/issues/778): Fixed NPE when exporting to .sql File


### Removed
- Fixed [#627](https://github.com/JabRef/jabref/issues/627): The pdf field is removed from the export formats, use the file field
- Removed configuration option to use database file directory as base directory for attached files and make it default instead.
{'fraction_non_alphanumeric': 0.10993630573248407, 'fraction_numerical': 0.028917197452229298, 'mean_word_length': 4.718135469774217, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 44, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5745811', 'n_tokens_mistral': 2538, 'n_tokens_neox': 2203, 'n_words': 863}