Clifton, 18, spent the 2016-17 season on loan with Grantham Town in the Evo-Stik League Northern Premier division.
He turned professional in July 2015 after coming through the academy, but is yet to play a game for the Mariners, who finished 14th this season.
However, Clifton has earned a new deal after impressing manager Russell Slade, who replaced Marcus Bignot in April.

BAM Nuttall handed over the project two years late in August 2011.
The council said it was left with £31m of defects on the St Ives to Cambridge route. It said while there were no safety concerns, the defects needed to be fixed.
No-one from BAM Nuttall was available to comment.
At a meeting of the general purposes committee, the council's technical advisers said the contractor should be held responsible for fixing problems including shallow foundations and inadequate drainage.
Although these were not dangerous, "ride quality would deteriorate" over time.
Councillors voted unanimously to begin legal action against BAM Nuttall.
It is estimated the repairs could take three years to complete.
The council originally paid BAM Nuttall £117.7m for its work.
However, last August after an on-going legal battle over the late delivery of the project, the company paid back £33m of that, reducing the cost to £84.7m.
Midfielder Harry Clifton has signed a one-year contract extension with League Two side Grimsby Town.
[NEXT_CONCEPT]
The company which built Cambridgeshire's guided busway is to be "held to account" for the cost of defects, the county council has agreed.