Now days, both the commercial and military sectors take FOD control very seriously. Every work task is performed according to a controlled procedure, whether it involves manufacturing, repair or maintenance. Hand tools required for a particular task are often placed on a "shadow board" prior to entering the FOD controlled work area, and just before leaving the FOD controlled work area the shadow board is checked to make sure no hand tools are missing.
Of course it wasn't always like this. Many years ago while working at an aircraft OEM, I recall the last thing done after assembling any enclosed structure was hoisting it vertically and shaking it to remove any loose debris. At the end of the assembly line there was a bulletin board where they displayed a plastic bag containing all of the FOD removed from each assembly. On one occasion I saw someones ID badge in the bag, which must have been embarrassing.