Do not package empty directories (#330)

Changes the packager to exclude any empty directories.

This change means that pkl project package for an already published packages will fail. The packager checks for an existing package at this version, and compares checksums. It will then error if the checksum has changed.

This is technically a breaking change, albeit a minor one. The workaround is to publish new versions of packages.

Published packages should still be compatible with Pkl 0.25.

pkl-cli/src/test/kotlin/org/pkl/cli/CliProjectPackagerTest.kt

@@ -241,7 +241,7 @@ class CliProjectPackagerTest {
               "type": "remote",
               "uri": "projectpackage://localhost:12110/birds@0.5.0",
               "checksums": {
-                "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+                "sha256": "04eec465b217fb9779489525d26e9b587e5e47ff4d584c7673a450109715bc31"
               }
             },
             "package://localhost:12110/fruit@1": {
@@ -332,7 +332,7 @@ class CliProjectPackagerTest {
         "version": "1.0.0",
         "packageZipUrl": "https://foo.com",
         "packageZipChecksums": {
-          "sha256": "7f515fbc4b229ba171fac78c7c3f2c2e68e2afebae8cfba042b12733943a2813"
+          "sha256": "e83b67722ea17ba41717ce6e99ae8ee02d66df6294bd319ce403075b1071c3e0"
         },
         "dependencies": {},
         "authors": []
@@ -344,9 +344,9 @@ class CliProjectPackagerTest {
     assertThat(expectedArchive.zipFilePaths())
       .hasSameElementsAs(listOf("/", "/c", "/c/d", "/c/d/foo.txt", "/a", "/a/b", "/a/b/foo.pkl"))
     assertThat(expectedMetadataChecksum)
-      .hasContent("203ef387f217a3caee7f19819ef2b50926929269241cb7b3a29d95237b2c7f4b")
+      .hasContent("72ab32b27393bde5f316b00f184faae919378e4d7643872c605f681b14b647bf")
     assertThat(expectedArchiveChecksum)
-      .hasContent("7f515fbc4b229ba171fac78c7c3f2c2e68e2afebae8cfba042b12733943a2813")
+      .hasContent("e83b67722ea17ba41717ce6e99ae8ee02d66df6294bd319ce403075b1071c3e0")
     FileSystems.newFileSystem(URI("jar:" + expectedArchive.toUri()), mutableMapOf<String, String>())
       .use { fs ->
         assertThat(fs.getPath("a/b/foo.pkl")).hasSameTextualContentAs(fooPkl)
@@ -364,6 +364,10 @@ class CliProjectPackagerTest {
       writeEmptyFile("main.test.pkl")
       writeEmptyFile("child/main.pkl")
       writeEmptyFile("child/main.test.pkl")
+      writeEmptyFile("examples/Workflow.pkl")
+      writeEmptyFile("examples/Ex1.pkl")
+      writeEmptyFile("tests/Test1.pkl")
+      writeEmptyFile("tests/integration/TestIng1.pkl")
     }
 
     tempDir.writeFile(
@@ -380,6 +384,8 @@ class CliProjectPackagerTest {
             "*.bin"
             "child/main.pkl"
             "*.test.pkl"
+            "examples/Ex1.pkl"
+            "tests/**"
           }
         }
       """
@@ -399,14 +405,12 @@ class CliProjectPackagerTest {
       .hasSameElementsAs(
         listOf(
           "/",
-          "/a",
+          "/examples",
-          "/a/b",
+          "/examples/Workflow.pkl",
-          "/a/b/c",
-          "/child",
           "/input",
           "/input/foo",
           "/input/foo/bar.txt",
-          "/main.pkl",
+          "/main.pkl"
         )
       )
   }
@@ -505,7 +509,7 @@ class CliProjectPackagerTest {
         "version": "1.0.0",
         "packageZipUrl": "https://foo.com",
         "packageZipChecksums": {
-          "sha256": "7d08a65078e0bfc382c16fe1bb94546ab9a11e6f551087f362a4515ca98102fc"
+          "sha256": "8739c76e681f900923b900c9df0ef75cf421d39cabb54650c4b9ad19b6a76d85"
         },
         "dependencies": {
           "birds": {
@@ -517,7 +521,7 @@ class CliProjectPackagerTest {
           "project2": {
             "uri": "package://localhost:12110/project2@5.0.0",
             "checksums": {
-              "sha256": "ddebb806e5b218ebb1a2baa14ad206b46e7a0c1585fa9863a486c75592bc8b16"
+              "sha256": "6f469b28f8b62a8a1191e2749bcf9c27dedbbb1e0ea754ac34af57b534e0ddda"
             }
           }
         },
@@ -537,7 +541,7 @@ class CliProjectPackagerTest {
       "version": "5.0.0",
       "packageZipUrl": "https://foo.com/project2.zip",
       "packageZipChecksums": {
-        "sha256": "7d08a65078e0bfc382c16fe1bb94546ab9a11e6f551087f362a4515ca98102fc"
+        "sha256": "8739c76e681f900923b900c9df0ef75cf421d39cabb54650c4b9ad19b6a76d85"
       },
       "dependencies": {},
       "authors": []
@@ -914,7 +918,7 @@ class CliProjectPackagerTest {
         """
       Package `package://localhost:12110/birds@0.5.0` was already published with different contents.
       
-      Computed checksum: 7324e17214b6dcda63ebfb57d5a29b077af785c13bed0dc22b5138628a3f8d8f
+      Computed checksum: 04eec465b217fb9779489525d26e9b587e5e47ff4d584c7673a450109715bc31
       Published checksum: 0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453
     """
           .trimIndent()

pkl-core/src/main/java/org/pkl/core/project/ProjectPackager.java

@@ -278,13 +278,6 @@ public class ProjectPackager {
     }
   }
 
-  private String ensureEndsWithSlash(Path file) {
-    if (file.endsWith("/")) {
-      return file.toString();
-    }
-    return file + "/";
-  }
-
   /**
    * Sets mtime to 0 so package creation is idempotent. Running the packager multiple times produces
    * the same output.
@@ -302,16 +295,10 @@ public class ProjectPackager {
     try (var zos = new ZipOutputStream(digestOutputStream)) {
       for (var file : files) {
         var relativePath = project.getProjectDir().relativize(file);
-        if (Files.isDirectory(file)) {
+        var zipEntry = new ZipEntry(relativePath.toString());
-          var zipEntry = new ZipEntry(ensureEndsWithSlash(relativePath));
+        zipEntry.setTime(ZIP_ENTRY_MTIME);
-          zipEntry.setTime(ZIP_ENTRY_MTIME);
+        zos.putNextEntry(zipEntry);
-          zos.putNextEntry(zipEntry);
+        Files.copy(file, zos);
-        } else {
-          var zipEntry = new ZipEntry(relativePath.toString());
-          zipEntry.setTime(ZIP_ENTRY_MTIME);
-          zos.putNextEntry(zipEntry);
-          Files.copy(file, zos);
-        }
         zos.closeEntry();
       }
     } catch (IOException e) {
@@ -344,6 +331,7 @@ public class ProjectPackager {
     var excludePatterns = getExcludePatterns(pkg);
     try (var stream = Files.walk(project.getProjectDir())) {
       return stream
+          .filter(Files::isRegularFile)
           .filter(
               (it) -> {
                 var fileNameRelativeToProjectRoot =