CQL execution improvements

.gitignore

@@ -9,6 +9,7 @@ docpath.txt
 
 *.log
 *.log.*
+LOG_FILE_IS_UNDEFINED
 .idea
 *.iml
 *.vsix

CHANGELOG.md

@@ -2,7 +2,30 @@
 
 ## v4.5.0
 
-Date: 2026-04-08
+Date: 2026-04-15
+
+### Execute CQL
+
+Adds a JSON-RPC–based Execute CQL command (`org.opencds.cqf.cql.ls.executeCql`) that
+replaces the previous CLI-based approach.
+
+* Accepts a structured `ExecuteCqlRequest` with per-library FHIR model paths, terminology URI,
+  context, and user-defined parameters
+* Evaluates all test cases for a library in a single batch (compile once, evaluate per patient)
+* `CqlEvaluator` — new evaluator that builds a shared engine per batch and runs each patient context
+* `DelegatingRepository` — mutable repository wrapper that swaps the patient bundle between evaluations
+* `ExecuteCqlCommandContribution` — registers the command and dispatches to `CqlEvaluator`
+* Removed `CliCommand` and `CqlCommand` (picocli CLI) — no longer needed
+* Returns structured JSON: expression results, server-side logs, and used-default-parameter metadata
+
+### Compilation Cache + Surgical Invalidation
+
+* `CqlCompilationManager` now caches compiled `CqlCompiler` results per source URI
+* Reverse dependency index tracks which URIs depend on each library identifier
+* `invalidate(uri)` evicts the URI and all dependents from the cache
+* `DiagnosticsService.didChangeWatchedFiles` triggers surgical invalidation on `.cql` file changes
+* `IgStandardRepository` adds a `typeResourceCache` — caches directory scans per resource
+  type/compartment combination, eliminating redundant filesystem walks across patients in a batch
 
 ### Module Consolidation
 

ls/server/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.opencds.cqf.cql.ls</groupId>
         <artifactId>cql-ls</artifactId>
-        <version>4.5.0-SNAPSHOT</version>
+        <version>4.5.0</version>
         <relativePath>../../pom.xml</relativePath>
     </parent>
 
@@ -88,11 +88,6 @@
             <artifactId>eventbus-java</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>info.picocli</groupId>
-            <artifactId>picocli</artifactId>
-        </dependency>
-
         <!-- Generated annotation -->
         <dependency>
             <groupId>jakarta.annotation</groupId>
@@ -153,31 +148,17 @@
                     </execution>
                 </executions>
             </plugin>
+            <!-- All source is Kotlin; checkstyle is a Java linter and has no work to do here. -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
         </plugins>
         <pluginManagement>
             <plugins>
-                <plugin>
-                    <groupId>org.jetbrains.kotlin</groupId>
-                    <artifactId>kotlin-maven-plugin</artifactId>
-                    <executions>
-                        <execution>
-                            <id>kapt</id>
-                            <goals><goal>kapt</goal></goals>
-                            <configuration>
-                                <sourceDirs>
-                                    <sourceDir>${project.basedir}/src/main/kotlin</sourceDir>
-                                </sourceDirs>
-                                <annotationProcessorPaths>
-                                    <annotationProcessorPath>
-                                        <groupId>info.picocli</groupId>
-                                        <artifactId>picocli-codegen</artifactId>
-                                        <version>${picocli.version}</version>
-                                    </annotationProcessorPath>
-                                </annotationProcessorPaths>
-                            </configuration>
-                        </execution>
-                    </executions>
-                </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-compiler-plugin</artifactId>
@@ -192,13 +173,6 @@
                             <arg>-Werror</arg>
                             <arg>-implicit:none</arg>
                         </compilerArgs>
-                        <annotationProcessorPaths>
-                            <path>
-                                <groupId>info.picocli</groupId>
-                                <artifactId>picocli-codegen</artifactId>
-                                <version>${picocli.version}</version>
-                            </path>
-                        </annotationProcessorPaths>
                     </configuration>
                 </plugin>
             </plugins>