Save As doesn't clear modified flag

[per1234]

Using Arduino IDE 1.6.13 Hourly Build 2016/10/21 05:33, Windows 7 64 bit

• Open a sketch
• Modify the sketch - the modified flag appears on the sketch tab
• File > Save As > Save - the modified flag still appears on the sketch tab

This will cause the IDE to unnecessarily prompt for a save on exit when the sketch has not been modified since the save as.

This issue doesn't occur with Arduino IDE 1.6.11 and previous versions, does occur in Arduino IDE 1.6.12.

EDIT: This issue also occurs with the test build 609 of #5528

[per1234]

@facchinm this issue still occurs with Arduino IDE 1.6.14 Hourly Build 2016/12/12 10:16