Code review comment: +1 , i'll make that change across all the commands.

Code under review:
public void execute() {
        if (this.helpFlag) {
            String commandUsageInfo = BLauncherCmd.getCommandUsageInfo(Constants.RUN_COMMAND);
            this.errStream.println(commandUsageInfo);
            return;
        }

        if (this.argList == null || this.argList.size() == 0) {
            CommandUtil.printError(this.errStream,
                    "no ballerina program given.",
                    "ballerina run {<bal-file> | <module-name>}",
                    true);
    
            Runtime.getRuntime().exit(1);
            return;
        }
    
        
        if (null != this.debugPort) {
            System.setProperty(SYSTEM_PROP_BAL_DEBUG, this.debugPort);
        }
        
        
        String[] programArgs = this.getProgramArgs(this.argList);
    
        
        Path sourceRootPath = this.sourceRoot == null ? Paths.get(System.getProperty("user.dir")) :
                              Paths.get(this.sourceRoot);
        Path sourcePath;
        Path targetPath;
    
        if (this.argList.get(0).endsWith(BLangConstants.BLANG_SRC_FILE_SUFFIX)) {
            
            
            if (Paths.get(this.argList.get(0)).isAbsolute()) {
                sourcePath = Paths.get(this.argList.get(0));
                sourceRootPath = sourcePath.getParent();
            } else {
                sourcePath = sourceRootPath.resolve(this.argList.get(0));
            }
    
            
            if (Files.notExists(sourcePath)) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' Ballerina file does not exist.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            
            if (!Files.isRegularFile(sourcePath)) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' is not a Ballerina file. check if it is a symlink or a shortcut.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            try {
                targetPath = Files.createTempDirectory("ballerina-run-" + System.nanoTime());
            } catch (IOException e) {
                throw LauncherUtils.createLauncherException("error occurred when creating executable.");
            }
        } else if (Files.exists(
                sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(this.argList.get(0))) &&
                   Files.isDirectory(
                           sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(this.argList.get(0)))) {
    
            
    
            
            if (!RepoUtils.isBallerinaProject(sourceRootPath)) {
                CommandUtil.printError(this.errStream,
                        "you are trying to run a module that is not inside a project.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            
            if (Paths.get(argList.get(0)).isAbsolute()) {
                CommandUtil.printError(this.errStream,
                        "you are trying to run a module by giving the absolute path. you only need give " +
                        "the name of the module.",
                        "ballerina run <module-name>",
                        true);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            String moduleName = argList.get(0);
    
            
            if (moduleName.endsWith("/")) {
                moduleName = moduleName.substring(0, moduleName.length() - 1);
            }
    
            sourcePath = Paths.get(moduleName);
    
            
            if (Files.notExists(sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(sourcePath))) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' module does not exist.",
                        "ballerina run <module-name>",
                        true);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            targetPath = sourceRootPath.resolve(ProjectDirConstants.TARGET_DIR_NAME);
        } else {
            CommandUtil.printError(this.errStream,
                    "invalid Ballerina source path, it should either be a module name in a Ballerina project, a " +
                    "file with a \'" + BLangConstants.BLANG_SRC_FILE_SUFFIX + "\' extension or a .jar file.",
                    "ballerina run {<bal-file> | <module-name>}",
                    true);
            Runtime.getRuntime().exit(1);
            return;
        }
    
        
        sourceRootPath = sourceRootPath.normalize();
        sourcePath = sourcePath == null ? null : sourcePath.normalize();
        targetPath = targetPath.normalize();
    
        
        CompilerContext compilerContext = new CompilerContext();
        CompilerOptions options = CompilerOptions.getInstance(compilerContext);
        options.put(PROJECT_DIR, sourceRootPath.toString());
        options.put(OFFLINE, Boolean.toString(this.offline));
        options.put(COMPILER_PHASE, CompilerPhase.BIR_GEN.toString());
        options.put(LOCK_ENABLED, Boolean.toString(true));
        options.put(SKIP_TESTS, Boolean.toString(true));
        options.put(TEST_ENABLED, "true");
        options.put(EXPERIMENTAL_FEATURES_ENABLED, Boolean.toString(this.experimentalFlag));

        
        BuildContext buildContext = new BuildContext(sourceRootPath, targetPath, sourcePath, compilerContext);
        buildContext.setOut(this.outStream);
        buildContext.setErr(this.errStream);
        
        boolean isSingleFileBuild = buildContext.getSourceType().equals(SINGLE_BAL_FILE);
    
        TaskExecutor taskExecutor = new TaskExecutor.TaskBuilder()
                .addTask(new CleanTargetDirTask(), isSingleFileBuild)   
                .addTask(new CreateTargetDirTask()) 
                .addTask(new CompileTask()) 
                .addTask(new CreateBaloTask(), isSingleFileBuild)   
                .addTask(new CreateBirTask())   
                .addTask(new CopyNativeLibTask())    
                .addTask(new CreateJarTask(false))  
                .addTask(new CopyModuleJarTask())
                .addTask(new CreateExecutableTask())  
                .addTask(new PrintExecutablePathTask(), isSingleFileBuild)   
                .addTask(new PrintRunningExecutableTask(!isSingleFileBuild))   
                .addTask(new RunExecutableTask(programArgs))
                .build();
    
        
        taskExecutor.executeTasks(buildContext);
    }

Line commented on: "invalid Ballerina source path, it should either be a module name in a Ballerina project, a " +

Revised code:
public void execute() {
        if (this.helpFlag) {
            String commandUsageInfo = BLauncherCmd.getCommandUsageInfo(Constants.RUN_COMMAND);
            this.errStream.println(commandUsageInfo);
            return;
        }

        if (this.argList == null || this.argList.size() == 0) {
            CommandUtil.printError(this.errStream,
                    "no ballerina program given.",
                    "ballerina run {<bal-file> | <module-name> | <executable-jar>}",
                    true);
    
            Runtime.getRuntime().exit(1);
            return;
        }
    
        
        if (null != this.debugPort) {
            System.setProperty(SYSTEM_PROP_BAL_DEBUG, this.debugPort);
        }
        
        
        String[] programArgs = this.getProgramArgs(this.argList);
    
        
        Path sourceRootPath = this.sourceRoot == null ? Paths.get(System.getProperty("user.dir")) :
                              Paths.get(this.sourceRoot);
        Path sourcePath;
        Path targetPath;
    
        if (this.argList.get(0).endsWith(BLangConstants.BLANG_SRC_FILE_SUFFIX)) {
            
            
            if (Paths.get(this.argList.get(0)).isAbsolute()) {
                sourcePath = Paths.get(this.argList.get(0));
                sourceRootPath = sourcePath.getParent();
            } else {
                sourcePath = sourceRootPath.resolve(this.argList.get(0));
            }
    
            
            if (Files.notExists(sourcePath)) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' Ballerina file does not exist.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            
            if (!Files.isRegularFile(sourcePath)) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' is not a Ballerina file. check if it is a symlink or a shortcut.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            try {
                targetPath = Files.createTempDirectory("ballerina-run-" + System.nanoTime());
            } catch (IOException e) {
                throw LauncherUtils.createLauncherException("error occurred when creating executable.");
            }
        } else if (Files.exists(
                sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(this.argList.get(0))) &&
                   Files.isDirectory(
                           sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(this.argList.get(0)))) {
    
            
    
            
            if (!RepoUtils.isBallerinaProject(sourceRootPath)) {
                CommandUtil.printError(this.errStream,
                        "you are trying to run a module that is not inside a project.",
                        null,
                        false);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            
            if (Paths.get(argList.get(0)).isAbsolute()) {
                CommandUtil.printError(this.errStream,
                        "you are trying to run a module by giving the absolute path. you only need give " +
                        "the name of the module.",
                        "ballerina run <module-name>",
                        true);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            String moduleName = argList.get(0);
    
            
            if (moduleName.endsWith("/")) {
                moduleName = moduleName.substring(0, moduleName.length() - 1);
            }
    
            sourcePath = Paths.get(moduleName);
    
            
            if (Files.notExists(sourceRootPath.resolve(ProjectDirConstants.SOURCE_DIR_NAME).resolve(sourcePath))) {
                CommandUtil.printError(this.errStream,
                        "'" + sourcePath + "' module does not exist.",
                        "ballerina run <module-name>",
                        true);
                Runtime.getRuntime().exit(1);
                return;
            }
    
            targetPath = sourceRootPath.resolve(ProjectDirConstants.TARGET_DIR_NAME);
        } else {
            CommandUtil.printError(this.errStream,
                    "invalid Ballerina source path. It should either be a name of a module in a Ballerina project, " +
                    "a file with a '" + BLangConstants.BLANG_SRC_FILE_SUFFIX + "' extension, or an executable '" +
                    BLANG_COMPILED_JAR_EXT + "' file.",
                    "ballerina run {<bal-file> | <module-name> | <executable-jar>}",
                    true);
            Runtime.getRuntime().exit(1);
            return;
        }
    
        
        sourceRootPath = sourceRootPath.normalize();
        sourcePath = sourcePath == null ? null : sourcePath.normalize();
        targetPath = targetPath.normalize();
    
        
        CompilerContext compilerContext = new CompilerContext();
        CompilerOptions options = CompilerOptions.getInstance(compilerContext);
        options.put(PROJECT_DIR, sourceRootPath.toString());
        options.put(OFFLINE, Boolean.toString(this.offline));
        options.put(COMPILER_PHASE, CompilerPhase.BIR_GEN.toString());
        options.put(LOCK_ENABLED, Boolean.toString(true));
        options.put(SKIP_TESTS, Boolean.toString(true));
        options.put(TEST_ENABLED, "true");
        options.put(EXPERIMENTAL_FEATURES_ENABLED, Boolean.toString(this.experimentalFlag));

        
        BuildContext buildContext = new BuildContext(sourceRootPath, targetPath, sourcePath, compilerContext);
        buildContext.setOut(this.outStream);
        buildContext.setErr(this.errStream);
        
        boolean isSingleFileBuild = buildContext.getSourceType().equals(SINGLE_BAL_FILE);
    
        TaskExecutor taskExecutor = new TaskExecutor.TaskBuilder()
                .addTask(new CleanTargetDirTask(), isSingleFileBuild)   
                .addTask(new CreateTargetDirTask()) 
                .addTask(new CompileTask()) 
                .addTask(new CreateBaloTask(), isSingleFileBuild)   
                .addTask(new CreateBirTask())   
                .addTask(new CopyNativeLibTask())    
                .addTask(new CreateJarTask(false))  
                .addTask(new CopyModuleJarTask())
                .addTask(new CreateExecutableTask())  
                .addTask(new PrintExecutablePathTask(), isSingleFileBuild)   
                .addTask(new PrintRunningExecutableTask(!isSingleFileBuild))   
                .addTask(new RunExecutableTask(programArgs))
                .build();
    
        
        taskExecutor.executeTasks(buildContext);
    }