address review comments

Signed-off-by: jorgee <jorge.ejarque@seqera.io>

Author: jorgee

modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy

@@ -46,7 +46,7 @@ class DefaultRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
     Path resolve(String moduleName) {
-        def baseDir = Global.session?.baseDir ?: Path.of('.')
+        def baseDir = Global.session?.baseDir ?: Path.of('.').toAbsolutePath()
         final config = Global.config ?: new ConfigBuilder().setBaseDir(baseDir).build()
         final registryConfig = config.navigate('registry') as RegistryConfig
 

modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy

@@ -161,7 +161,7 @@ class ModuleResolver {
             // Install to modules directory (will compute directory checksum for future integrity checks)
             InstalledModule installed = storage.installModule(reference, version, tempFile, downloadUrl)
 
-            log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent.toAbsolutePath().toString()}"
+            log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent.toAbsolutePath()}"
             return installed.mainFile
         }
         finally {

modules/nf-lang/src/main/java/nextflow/module/spi/FallbackRemoteModuleResolver.java

@@ -31,18 +31,15 @@
 public class FallbackRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-<<<<<<< fix-module-system-basedir
     public Path resolve(String moduleName) {
-        final Path baseDir = Path.of("modules");
-        if (!Files.exists(baseDir.resolve(moduleName))) {
-            throw new IllegalStateException("Module '" + moduleName + "' not locally found at 'modules' folder - use 'nextflow install' to download module files");
-=======
-    public Path resolve(String moduleName, Path baseDir) {
+        // Use CWD-relative "modules" directory as a best-effort fallback when no
+        // RemoteModuleResolver SPI implementation is available (e.g. running outside
+        // a full Nextflow session).
+        final Path baseDir = Path.of("modules").toAbsolutePath();
         final var resolved = baseDir.resolve(moduleName).normalize();
         // Prevent path traversal outside the base directory
         if (!resolved.startsWith(baseDir.normalize())) {
             throw new IllegalStateException("Invalid module name '" + moduleName + "' - path escapes the modules directory");
->>>>>>> master
         }
         if (!Files.exists(resolved)) {
             throw new IllegalStateException("Module '" + moduleName + "' not locally found at 'modules' folder - use 'nextflow module install' to download module files");

modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java

@@ -87,9 +87,19 @@ public void visitInclude(IncludeNode node) {
             return;
         }
 
-        var includeUri = ModuleResolver.isRemoteModule(source) ?
-            RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri() :
-            getIncludeUri(Path.of(sourceUnit.getSource().getURI()).getParent(), source);
+        URI includeUri;
+        if( ModuleResolver.isRemoteModule(source) ) {
+            try {
+                includeUri = RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri();
+            }
+            catch( IllegalStateException e ) {
+                addError(e.getMessage(), node);
+                return;
+            }
+        }
+        else {
+            includeUri = getIncludeUri(Path.of(sourceUnit.getSource().getURI()).getParent(), source);
+        }
         if( !isIncludeStale(node, includeUri) )
             return;
         changed = true;