SANTA CLARA, Calif. — The reconstruction of the San Francisco 49ers roster since coach Kyle Shanahan and general manager John Lynch arrived in January of 2017 was swift and far-reaching.

Aside from the actual facilities in which the 49ers practice and play games, the only remaining remnants of the previous regime are the 13 players still on the 90-man roster. To drive the point home further, only left tackle Joe Staley and tight end Garrett Celek remain from the team that came up just short in Super Bowl XLVII on Feb. 3, 2013.

John Lynch and Kyle Shanahan have often valued youth in their roster overhaul. Tim Warner/Getty Images

“We feel a lot better than this time last year,” Lynch said. “… We’re a much more talented team. I think we’re a deeper team. We went into the draft and one of the things is, we’re still looking for game changers. That will always be important, but I think to be able to put pieces to the puzzle before last year there were many times where it’s like, ‘We’ve got to find a slot receiver. We’ve got to find this, we’ve got to find that.’ Now, it’s just like, ‘Who is the best player and who fits what we do the best?’”

For those keeping score at home, the Trent Baalke baker’s dozen consists of Staley, defensive tackle DeForest Buckner, end Arik Armstead, guard Joshua Garnett, defensive back Jimmie Ward, running back Raheem Mostert, wide receiver Aaron Burbridge, linebacker Eli Harold, Celek, defensive lineman Ronald Blair III, safety Jaquiski Tartt, punter Bradley Pinion and long snapper Kyle Nelson.

Of that group, Staley, Buckner, Armstead, Harold and Tartt project as starters on offense or defense, with Pinion and Nelson also expected to continue in their roles. And though it’s possible the others could make the 53-man roster, some figure to have to battle until the end of the preseason.

“I’ve been happy with what we’ve done in our two-year span, just getting guys, some of our later draft picks, some undrafted guys, some of our free agents,” Shanahan said. “I’m glad these guys have come in and been able to help us do that because you can’t just turn over a roster until you have people to replace them with. So, you’re always looking to upgrade, whatever it is. We’re still looking to do that. I hope that gets harder and harder for us each year.”

But the true test of how far the Niners’ roster has come since Shanahan and Lynch took over (aside, of course, from their performance on the field) might be what happens when the roster gets cut down.

Last year, Lynch and Shanahan were able to sell potential additions on what Lynch called a “land of opportunity.” In other words, there were plenty of vacancies and any able-bodied player was welcome to apply. In the first two months after they were hired, they signed, drafted or traded for 50 players, accounting for 55 percent of the 90-man roster.

When it came time to trim the roster, nine of the team’s 10 drafted rookies made the initial 53 and the lone exception — running back Joe Williams — landed on injured reserve and has returned this season. In addition, eight undrafted rookies spent at least a chunk of the season on the active roster. Three more stayed with the team via injured reserve. Seventeen Niners rookies combined to play a league-high 4,798 snaps.

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While the first year of the rebuild offered plenty of chances for those young players to get opportunities, it also gave the Niners a chance to evaluate what they needed to add in the second offseason. Of the 37 players waived or released last year, the only further football opportunity for many came in the form of practice-squad jobs in San Francisco or re-signing with the team later in the season after injuries began to pile up.

Looking back on those who were let go, only defensive lineman Quinton Dial, wide receiver Jeremy Kerley, tight end Blake Bell and quarterback Matt Barkley ended up spending any significant time on any other active rosters during the 2017 season. And Barkley signed with Arizona only after a series of quarterback injuries.

Put simply, the 49ers were often able to err on the side of youth with their roster decisions because they simply didn’t have that many talented players to pick from. Thus, it made more sense to opt for someone with upside rather than someone who had already proved unable to make a difference.

This year, Shanahan believes there are difficult decisions to be made.

“I always like to go in the beginning of camp and look at the whole roster,” Shanahan said. “… Look at ‘OK, how many NFL players do we have on our roster that we’re going to have to cut?’ What’s different about this year is the depth. We’re going to have to cut some guys who are going to go play for other people this year. It’s a tough thing at the end, but it’s our goal. That’s what you want.”