diff --git a/phpunit/src/CompilerBaseApiTest.php b/phpunit/src/CompilerBaseApiTest.php
index 080d0078..ddcaa871 100644
--- a/phpunit/src/CompilerBaseApiTest.php
+++ b/phpunit/src/CompilerBaseApiTest.php
@@ -232,7 +232,7 @@ YAML);
         $this->assertTrue($this->getPropertyValue('noLiteralStrings'));
         $this->assertSame('address', $this->getPropertyValue('sanitize'));
         $this->assertSame('aarch64-linux-gnu', $this->getPropertyValue('targetPlatform'));
-        $this->assertSame(['/opt/mylib/include', '../shared/headers'], $this->compiler->getUserIncludePaths());
+        $this->assertSame(['/opt/mylib/include', dirname($projectFile) . '/../shared/headers'], $this->compiler->getUserIncludePaths());
         $this->assertSame(['ENABLE_LOGGING=1', 'DEBUG_LEVEL=3'], $this->compiler->getUserDefines());
         $this->assertTrue($this->compiler->isLtoEnabled());
         $this->assertSame(['curl', 'ssl'], $this->compiler->getLinkLibs());
@@ -272,7 +272,58 @@ YAML, 'custom-name.yml', 'yaml-alias');
         $this->assertSame(CompilerBase::BUILD_MODE_EXT, $this->getPropertyValue('buildMode'));
         $this->assertTrue($this->getPropertyValue('dryRun'));
         $this->assertSame('custom_ext', $this->getPropertyValue('targetName'));
-        $this->assertSame('out', $this->getPropertyValue('outputDir'));
+        $this->assertSame(dirname($projectFile) . '/out', $this->getPropertyValue('outputDir'));
+    }
+
+    public function testParseProjectYamlResolvesRelativePathOptionsAgainstYamlDirectory(): void
+    {
+        $projectFile = $this->createProjectFile(<<<'YAML'
+sources:
+  - main.php
+include-paths:
+  - includes
+link-paths:
+  - libs
+output: bin/my-app
+YAML, 'myproject.yml', 'nested/config');
+
+        $this->invokeMethod('parseProjectYaml', $projectFile);
+
+        $projectDir = dirname($projectFile);
+        $this->assertSame([$projectDir . '/includes'], $this->compiler->getUserIncludePaths());
+        $this->assertSame([$projectDir . '/libs'], $this->compiler->getLinkPaths());
+        $this->assertSame($projectDir . '/bin', $this->getPropertyValue('outputDir'));
+        $this->assertSame('my_app', $this->getPropertyValue('targetName'));
+    }
+
+    public function testCliOutputOverridesYamlOutputOnlyWhenCommandLineArgumentsAreApplied(): void
+    {
+        global $argv;
+        $argv = ['compiler.php', '--output', 'cli/out-file'];
+        $compiler = CompilerTest::create($this->testDir);
+        $ref = new \ReflectionClass($compiler);
+        $parseMethod = $ref->getMethod('parseProjectYaml');
+        $parseMethod->setAccessible(true);
+        $applyMethod = $ref->getMethod('applyCommandLineArguments');
+        $applyMethod->setAccessible(true);
+        $targetProp = $ref->getProperty('targetName');
+        $targetProp->setAccessible(true);
+        $outputProp = $ref->getProperty('outputDir');
+        $outputProp->setAccessible(true);
+
+        $projectFile = $this->createProjectFile(<<<'YAML'
+sources:
+  - main.php
+output: yaml/out-file
+YAML, 'myproject.yml', 'cli-output');
+
+        $parseMethod->invoke($compiler, $projectFile);
+        $this->assertSame(dirname($projectFile) . '/yaml', $outputProp->getValue($compiler));
+        $this->assertSame('out_file', $targetProp->getValue($compiler));
+
+        $applyMethod->invoke($compiler);
+        $this->assertSame('cli', $outputProp->getValue($compiler));
+        $this->assertSame('out_file', $targetProp->getValue($compiler));
     }
 
     public function testApplyCommandLineArgumentsDoesNotClearYamlRepeatableOptionsWhenCliAbsent(): void
@@ -301,6 +352,29 @@ YAML);
         $this->assertSame(['/yaml/lib'], $this->compiler->getLinkPaths());
     }
 
+    public function testParseProjectYamlFiltersIgnoredFilesFromReturnedSources(): void
+    {
+        $projectFile = $this->createProjectFile(<<<'YAML'
+sources:
+  - .
+ignore:
+  - ignored.php
+  - skipped
+YAML);
+        $projectDir = dirname($projectFile);
+        mkdir($projectDir . '/skipped', 0777, true);
+        file_put_contents($projectDir . '/ignored.php', "<?php\nfunction ignored() {}\n");
+        file_put_contents($projectDir . '/skipped/nested.php', "<?php\nfunction skipped() {}\n");
+        file_put_contents($projectDir . '/kept.php', "<?php\nfunction kept() {}\n");
+
+        $files = $this->invokeMethod('parseProjectYaml', $projectFile);
+
+        $this->assertContains(realpath($projectDir . '/main.php'), $files);
+        $this->assertContains(realpath($projectDir . '/kept.php'), $files);
+        $this->assertNotContains(realpath($projectDir . '/ignored.php'), $files);
+        $this->assertNotContains(realpath($projectDir . '/skipped/nested.php'), $files);
+    }
+
     public function testCCompileCommandOptionsKeepCommonUserConfiguration(): void
     {
         $this->setPropertyValue('userIncludePaths', ['/user/include']);
diff --git a/src/Php/Translator.php b/src/Php/Translator.php
index 877a8031..dc5401cc 100644
--- a/src/Php/Translator.php
+++ b/src/Php/Translator.php
@@ -325,6 +325,11 @@ class Translator extends Preprocessor
             $this->targetPlatform = $this->climate->arguments->get('target-platform');
         }
 
+        // 输出文件名/路径
+        if ($this->climate->arguments->defined('output')) {
+            $this->setTargetName($this->climate->arguments->get('output'));
+        }
+
         // 构建目录
         if ($this->climate->arguments->defined('build-dir')) {
             $buildDir = $this->climate->arguments->get('build-dir');
@@ -546,9 +551,6 @@ class Translator extends Preprocessor
 
     public function setTargetName(string $name): void
     {
-        if ($this->climate->arguments->defined('output')) {
-            $name = $this->climate->arguments->get('output');
-        }
         // 如果指定了路径（包含目录分隔符），提取目录和文件名
         if (str_contains($name, '/') || str_contains($name, '\\')) {
             $this->outputDir = dirname($name);
@@ -609,7 +611,7 @@ class Translator extends Preprocessor
         // 在所有配置加载完成后，应用命令行参数（确保优先级最高）
         $this->applyCommandLineArguments();
 
-        return $list;
+        return $this->filterIgnoredFiles($list);
     }
 
     public function prepare(string $path): array
@@ -627,20 +629,7 @@ class Translator extends Preprocessor
         }
 
         $files = $this->getFiles($path);
-        // 应用 ignorePaths 过滤
-        if (!empty($this->ignorePaths)) {
-            $files = array_filter($files, function ($file) {
-                foreach ($this->ignorePaths as $ignorePath) {
-                    if ($file === $ignorePath) {
-                        return false;
-                    }
-                    if (is_dir($ignorePath) && str_starts_with($file, $ignorePath . DIRECTORY_SEPARATOR)) {
-                        return false;
-                    }
-                }
-                return true;
-            });
-        }
+        $files = $this->filterIgnoredFiles($files);
         // 分析 PHP 文件，预处理
         foreach ($files as $k => $file) {
             if (FileScanner::isPhpFile($file)) {
@@ -659,6 +648,29 @@ class Translator extends Preprocessor
         return $files;
     }
 
+    protected function shouldIgnoreFile(string $file): bool
+    {
+        foreach ($this->ignorePaths as $ignorePath) {
+            if ($file === $ignorePath) {
+                return true;
+            }
+            if (is_dir($ignorePath) && str_starts_with($file, rtrim($ignorePath, DIRECTORY_SEPARATOR) . DIRECTORY_SEPARATOR)) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
+    protected function filterIgnoredFiles(array $files): array
+    {
+        if (empty($this->ignorePaths)) {
+            return $files;
+        }
+
+        return array_values(array_filter($files, fn(string $file): bool => !$this->shouldIgnoreFile($file)));
+    }
+
     public function convert(array $files): array
     {
         $sourceFiles = [];
@@ -2071,7 +2083,7 @@ CODE;
         $includePaths = $cfg['include-paths'] ?? null;
         if (!empty($includePaths) && is_array($includePaths)) {
             foreach ($includePaths as $includePath) {
-                $this->userIncludePaths[] = (string) $includePath;
+                $this->userIncludePaths[] = $this->resolvePath((string) $includePath, $projectDir, 'Include path');
             }
         }
 
@@ -2105,14 +2117,14 @@ CODE;
         $linkPaths = $cfg['link-paths'] ?? null;
         if (!empty($linkPaths) && is_array($linkPaths)) {
             foreach ($linkPaths as $linkPath) {
-                $this->linkPaths[] = (string)$linkPath;
+                $this->linkPaths[] = $this->resolvePath((string) $linkPath, $projectDir, 'Link path');
             }
         }
 
         // 读取 output/name
         $output = $cfg['output'] ?? $cfg['name'] ?? null;
         if (!empty($output)) {
-            $this->setTargetName((string) $output);
+            $this->setTargetName($this->resolvePath((string) $output, $projectDir, 'Output path'));
         }
 
         // 读取 cpp-compiler
@@ -2175,7 +2187,7 @@ CODE;
             $this->resourceConfig['_projectDir'] = $projectDir;
         }
 
-        return $list;
+        return $this->filterIgnoredFiles($list);
     }
 
     protected function getInternalCeInfo(string $ce): array