ScipWriter.close() / ScipOutputStream never closes the underlying OutputStream before Files.move(), leaking file descriptors and locking temp files on Windows #1066

Summary

In scip-aggregator, ScipWriter implements AutoCloseable and writes to a temporary file (tmp) via ScipOutputStream(new BufferedOutputStream(Files.newOutputStream(tmp))), then moves tmp to options.output() in ScipWriter.build().

However, ScipWriter.close() only calls output.flush(), and ScipOutputStream has no close() method at all. The underlying OutputStream to tmp is never closed before Files.move(tmp, options.output(), StandardCopyOption.REPLACE_EXISTING) runs.

Affected Code (main)

• scip-aggregator/src/main/java/org/scip_code/scip_java/aggregator/ScipWriter.java (lines 20–40):

  this.output = new ScipOutputStream(new BufferedOutputStream(Files.newOutputStream(tmp)));
  ...
  public void build() throws IOException {
    close();
    Files.move(tmp, options.output(), StandardCopyOption.REPLACE_EXISTING);
  }
  
  @Override
  public void close() throws IOException {
    output.flush();
  }

• scip-aggregator/src/main/java/org/scip_code/scip_java/aggregator/ScipOutputStream.java (lines 9–36):
  Wraps private final OutputStream out; and exposes write(...) and flush(), but does not implement AutoCloseable or provide a close() method.

Impact

1. Windows (win32) file lock failures: When ScipWriter.build() calls Files.move(tmp, options.output(), StandardCopyOption.REPLACE_EXISTING) while the OutputStream handle on tmp is still open — especially when %TEMP% (e.g. C:\Users\...\AppData\Local\Temp) and --output (e.g. D:\workspace\index.scip or another mount/volume) are on different drives, forcing Files.move to copy + Files.delete(tmp) — Windows fails with:

   java.nio.file.FileSystemException: <tmp> -> <output>: The process cannot access the file because it is being used by another process
   

2. Resource leak on all platforms: Every ScipWriter instance leaks an open file descriptor until GC/process exit.
3. Note on Fix ScipWriter temp file creation on file systems without POSIX permissions #1049: Once Fix ScipWriter temp file creation on file systems without POSIX permissions #1049 fixes the PosixFilePermissions crash in ScipWriter on Windows, ScipWriter.build() immediately hits this unclosed stream during Files.move.

Suggested Fix

1. Implement AutoCloseable (or add close()) on ScipOutputStream:

   public void close() throws IOException {
     flush();
     out.close();
   }

2. Call output.close() in ScipWriter.close():

   @Override
   public void close() throws IOException {
     output.close();
   }