Review/fix/change file reassembly functionality.

- Re-arrange how some fa_file fields (e.g. source, connection info, mime
  type) get updated/set for consistency.

- Add more robust mechanisms for flushing the reassembly buffer.
  The goal being to report all gaps and deliveries to file analyzers
  regardless of the state of the reassembly buffer at the time it has to
  be flushed.

src/file_analysis/FileReassembler.h

@@ -11,9 +11,6 @@ namespace file_analysis {
 
 class File;
 
-//const int STOP_ON_GAP = 1;
-//const int PUNT_ON_PARTIAL = 1;
-
 class FileReassembler : public Reassembler {
 public:
 
@@ -21,12 +18,35 @@ public:
 	virtual ~FileReassembler();
 
 	void Done();
-	uint64 GetFirstBlockOffset() { return blocks->seq; }
 
 	// Checks if we have delivered all contents that we can possibly
 	// deliver for this endpoint.
 	void CheckEOF();
 
+	/**
+	 * Discards all contents of the reassembly buffer.  This will spin through
+	 * the buffer and call File::DeliverStream() and File::Gap() wherever
+	 * appropriate.
+	 * @return the number of new bytes now detected as gaps in the file.
+	 */
+	uint64 Flush();
+
+	/**
+	 * Discards all contents of the reassembly buffer up to a given sequence
+	 * number.  This will spin through the buffer and call
+	 * File::DeliverStream() and File::Gap() wherever appropriate.
+	 * @param sequence the sequence number to flush until.
+	 * @return the number of new bytes now detected as gaps in the file.
+	 */
+	uint64 FlushTo(uint64 sequence);
+
+	/**
+	 * @return whether the reassembler is currently is the process of flushing
+	 * out the contents of its buffer.
+	 */
+	bool IsCurrentlyFlushing() const
+		{ return flushing; }
+
 protected:
 	FileReassembler()	{ }
 
@@ -36,10 +56,8 @@ protected:
 	void BlockInserted(DataBlock* b);
 	void Overlap(const u_char* b1, const u_char* b2, uint64 n);
 
-	unsigned int had_gap:1;
-	unsigned int did_EOF:1;
-	unsigned int skip_deliveries:1;
 	File* the_file;
+	bool flushing;
 };
 
 } // namespace analyzer::*