Merge remote-tracking branch 'upstream/main' into dbsync

* upstream/main:
  Fix parsing of JabRef v5.7 study.yml files (#9124)
  Fix integrity check  for tilde accents in author names (#9097)
  Rework the Define study parameters dialog (#9123)
  Fix parsing of save actions (#9122)
  Fix exception that occurs when saving name formatters (#9121)
  Refine code for BibEntry#replaceDownloadedFile (#9118)

CHANGELOG.md

@@ -24,13 +24,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We call backup files `.bak` and temporary writing files now `.sav`.
 - JabRef keeps 10 older versions of a `.bib` file in the [user data dir](https://github.com/harawata/appdirs#supported-directories) (instead of a single `.sav` (now: `.bak`) file in the directory of the `.bib` file)
 - We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
-- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs.
+- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
+- A user can now add arbitrary data into `study.yml`. JabRef just ignores this data. [#9124](https://github.com/JabRef/jabref/pull/9124)
 - We reworked the External Changes Resolver dialog. [#9021](https://github.com/JabRef/jabref/pull/9021)
-
+- We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 
 ### Fixed
 
-- We fixed an issue where the possibilty to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
+- We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
+- We fixed an issue where the possibility to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
 - We fixed the display of issue, number, eid and pages fields in the entry preview. [#8607](https://github.com/JabRef/jabref/pull/8607), [#8372](https://github.com/JabRef/jabref/issues/8372), [Koppor#514](https://github.com/koppor/jabref/issues/514), [forum#2390](https://discourse.jabref.org/t/unable-to-edit-my-bibtex-file-that-i-used-before-vers-5-1/2390), [forum#3462](https://discourse.jabref.org/t/jabref-5-6-need-help-with-export-from-jabref-to-microsoft-word-entry-preview-of-apa-7-not-rendering-correctly/3462)
 - We fixed the page ranges checker to detect article numbers in the pages field (used at [Check Integrity](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity)). [#8607](https://github.com/JabRef/jabref/pull/8607)
 - The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
@@ -39,8 +41,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed some visual glitches with the linked files editor field in the entry editor and increased its height. [#8823](https://github.com/JabRef/jabref/issues/8823)
 - We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#9067](https://github.com/JabRef/jabref/pull/9067), [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
 - We fixed an issue where applied save actions on saving the library file would lead to the dialog "The libary has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
-- We fixed an issue where title case didn't capitalize words after en-dash characters [#9068]
-- We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open [#9075](https://github.com/JabRef/jabref/issues/9075)
+- We fixed issues with save actions not correctly loaded when opening the library. [#9122](https://github.com/JabRef/jabref/pull/9122)
+- We fixed an issue where title case didn't capitalize words after en-dash characters. [#9068](https://github.com/JabRef/jabref/pull/9068)
+- We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open. [#9075](https://github.com/JabRef/jabref/issues/9075)
 
 ### Removed
 
@@ -107,6 +110,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed a bug where updating group view mode (intersection or union) requires re-selecting groups to take effect. [#6998](https://github.com/JabRef/jabref/issues/6998)
 - We fixed a bug that prevented external group metadata changes from being merged. [#8873](https://github.com/JabRef/jabref/issues/8873)
 - We fixed the shared database opening dialog to remember autosave folder and tick. [#7516](https://github.com/JabRef/jabref/issues/7516)
+- We fixed an issue where name formatter could not be saved. [#9120](https://github.com/JabRef/jabref/issues/9120)
 
 ### Removed
 

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -454,13 +454,12 @@ public void download() {
                 }
 
                 if (!isDuplicate) {
+                    // we need to call LinkedFileViewModel#fromFile, because we need to make the path relative to the configured directories
                     LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(
                             destination,
                             databaseContext.getFileDirectories(preferences.getFilePreferences()),
                             preferences.getFilePreferences());
-                    List<LinkedFile> linkedFiles = entry.getFiles();
-
-                    entry.addLinkedFile(entry, linkedFile, newLinkedFile, linkedFiles);
+                    entry.replaceDownloadedFile(linkedFile.getLink(), newLinkedFile);
 
                     // Notify in bar when the file type is HTML.
                     if (newLinkedFile.getFileType().equals(StandardExternalFileType.URL.getName())) {