Merge upstream/main, fix submodules

Author: alexsukhin

.idea/checkstyle-idea.xml

@@ -34,10 +34,10 @@
 //DEPS org.jspecify:jspecify:1.0.0
 
 // from jabls
+//DEPS com.fasterxml.jackson.core:jackson-databind:2.20.0
 //DEPS com.github.eclipse:lsp4j:0.24.0
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.2
-//DEPS org.hisp.dhis:json-tree:1.8.1
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS org.slf4j:jul-to-slf4j:2.0.17
 //DEPS org.slf4j:slf4j-api:2.0.17

.idea/vcs.xml

@@ -463,10 +463,6 @@ extraJavaModuleInfo {
         requires("java.logging")
     }
 
-    module("org.hisp.dhis:json-tree", "org.hisp.dhis.jsontree") {
-        preserveExisting()
-    }
-
     module("com.github.sialcasa.mvvmFX:mvvmfx-validation", "de.saxsys.mvvmfx.validation") {
         exportAllPackages()
         requireAllDefinedDependencies()

.jbang/JabLsLauncher.java

@@ -9,6 +9,7 @@
 //DEPS org.openjfx:javafx-base:24.0.1
 //DEPS org.slf4j:slf4j-api:2.0.13
 //DEPS org.slf4j:slf4j-simple:2.0.13
+//DEPS org.jspecify:jspecify:1.0.0
 
 //SOURCES ../../../../jablib/src/main/java/org/jabref/logic/journals/Abbreviation.java
 //SOURCES ../../../../jablib/src/main/java/org/jabref/logic/journals/AbbreviationFormat.java

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -7,6 +7,7 @@
 //DEPS info.debatty:java-string-similarity:2.0.0
 //DEPS org.jooq:jool:0.9.14
 //DEPS org.openjfx:javafx-base:24.0.1
+//DEPS org.jspecify:jspecify:1.0.0
 //DEPS org.slf4j:slf4j-api:2.0.13
 //DEPS org.slf4j:slf4j-simple:2.0.13
 

build-support/src/main/java/JournalListMvGenerator.java

@@ -68,8 +68,8 @@ public String getHeading() {
 * Create constructor which initializes the fields to their default values. Write tests to ensure that everything works as expected!
 
 ```java
-public MyDialogViewModel(Dependency dependency) {
-    this.dependency = Objects.requireNonNull(dependency);
+public MyDialogViewModel(@NonNull Dependency dependency) {
+    this.dependency = dependency;
     heading.set("Hello " + dependency.getUserName());
 }
 ```

build-support/src/main/java/LtwaListMvGenerator.java

@@ -12,13 +12,14 @@ When trying to parse nested JSON structures in JabLS which receives the VSCode s
 ## Considered Options
 
 * Use `org.hisp.dhis:json-tree`
+* Use Jackson
 * Use Unirest and Optional
 * Use GSON and chaining Optional
 * Use an own method to parse the path
 
 ## Decision Outcome
 
-Chosen option: "Use `org.hisp.dhis:json-tree`", because comes out best (see below).
+Chosen option: "Use Jackson" because it comes out best (see below).
 
 ## Pros and Cons of the Options
 
@@ -34,6 +35,17 @@ this.integrityCheck = json.getBoolean("jabref.integrityCheck.enabled").booleanVa
 * Good, because it has a fallback value
 * Bad, because it introduces a new dependency
 
+### Use Jackson
+
+```java
+this.consistencyCheck = node.at("/jabref/consistencyCheck/enabled").asBoolean(this.consistencyCheck);
+```
+
+* Good, because very compact and readable
+* Good, because no Exception is thrown if path does not exist
+* Good, because it supports nested paths directly
+* Good, because it has a fallback value
+
 ### Use Unirest and Optional
 
 ```java

docs/code-howtos/javafx.md

@@ -0,0 +1,79 @@
+---
+title: Adopt JSpecify nullness annotations for compile-time null safety
+nav_order: 51
+parent: Decision Records
+status: pending
+---
+
+# Adopt JSpecify nullness annotations for compile-time null safety
+
+## Context and Problem Statement
+
+Our Java codebase contains inconsistent handling of nullability.
+We want to detect null-safety issues earlier at compile time and improve API clarity.
+
+## Decision Drivers
+
+* Reduce `NullPointerException`s in production by shifting detection to compile time.
+* Provide clearer API contracts.
+* Keep runtime overhead low.
+* Ensure incremental and low-risk adoption.
+
+## Considered Options
+
+* Do nothing and keep status quo.
+* Use `Objects.requireNonNull` and defensive runtime checks.
+* Adopt JSpecify annotations.
+* Use `assert x == null`.
+
+## Decision Outcome
+
+Chosen option: "Adopt JSpecify annotations" because comes out best (see below).
+
+## Consequences
+
+* Earlier detection of potential NPEs.
+* Clearer API documentation.
+* Requires training and CI integration.
+* Some friction with unannotated third-party libraries.
+
+## Pros and Cons of the Options
+
+### Do nothing and keep status quo
+
+* Good, because no immediate implementation work.
+* Bad, because NPEs remain runtime-only problems.
+* Bad, because a mix of different approaches leads to bad code.
+* Bad, because it increases technical debt.
+* Bad, because assumes that non-annotated symbols allow null.
+
+### Use `Objects::requireNonNull`
+
+* Good, because JDK native.
+* Good, because no external dependencies.
+* Good, because it makes NPEs more visible on runtime.
+* Bad, because it adds runtime overhead.
+* Bad, because it does not provide compile-time contracts.
+* Bad, because it is not self-documenting for API contract.
+
+### Adopt JSpecify annotations
+
+* Good, because it offers compile-time null safety detection.
+* Good, because it works well with common IDEs.
+* Good, because of standardized annotations.
+* Good, because incremental adoption possible.
+* Good, because static analysis supported.
+* Good, because compatibility with Kotlin.
+* Good, because it is the consensus among major organizations (Google, Microsoft, Jetbrains etc).
+* Bad, because it requires annotation effort.
+* Bad, because it requires developer training.
+
+### Use `assert x == null`
+
+* Good, because Java language native.
+* Good, because no external dependencies.
+* Good, because easily readable.
+* Good, because it makes NPEs more visible on runtime.
+* Bad, because runs by default only in debug mode with option "-ea".
+* Bad, because it does not provide compile-time null safety.
+* Bad, because it is not self-documenting for API contract.

docs/decisions/0051-handle-nested-json-paths.md

@@ -2,7 +2,6 @@
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Objects;
 import java.util.Optional;
 import java.util.function.Function;
 
@@ -45,6 +44,7 @@
 import com.tobiasdiez.easybind.EasyBind;
 import com.tobiasdiez.easybind.EasyBinding;
 import com.tobiasdiez.easybind.PreboundBinding;
+import org.jspecify.annotations.NonNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -144,8 +144,7 @@ public void setSelectedEntries(List<BibEntry> newSelectedEntries) {
     }
 
     @Override
-    public void setSelectedGroups(BibDatabaseContext context, List<GroupTreeNode> newSelectedGroups) {
-        Objects.requireNonNull(newSelectedGroups);
+    public void setSelectedGroups(BibDatabaseContext context, @NonNull List<GroupTreeNode> newSelectedGroups) {
         selectedGroups.computeIfAbsent(context.getUid(), k -> FXCollections.observableArrayList()).setAll(newSelectedGroups);
     }