feat!: make --empty-repo default

[hacdias]

Closes #9757.

• Makes --empty-repo default
• Flips the tests with that flag
• Updates sharness tests that require the default docs

[lidel]

I suspect this will break a lot of naive tests outside this repo,
but this is the price for cleaning this up and paying off the technical debt.

Flipping the flag first is a smart way of doing this.
We can ship it, people can still restore old behavior by passing ipfs init --empty-repo=false if they need to fix their tests.

cc @yiannisbot @dennis-tra for visibility – the CIDs that every Kubo had pinned and announced by default will no longer be present, so we can't rely on them for fingerprinting Kubo instances anymore.

Before

$ ipfs init && ipfs refs local
generating ED25519 keypair...done
peer identity: 12D3KooWNgbPevBVzHPyQTEs81dG2JvDnJKwtcbzhAPQ7hfpPCJp
initializing IPFS node at /home/lidel/tmp/test-refactor-1680267541
to get started, enter:

	ipfs cat /ipfs/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/readme

bafkreiasgpw5ago4iqge4p3bupju6gdmelkqqpxxljax4fcg4ouffnep64
bafkreiczsscdsbs7ffqz55asqdf3smv6klcw3gofszvwlyarci47bgf354
bafkreihtwdtifv43rn5cyilnmkwofdcxi2suqimmo62vn3etf45gjoiuwy
bafkreib6ofpfz3wpht3fnitq5tnkrmcxwkqzqfso75djgcjutauzsfsvce
bafkreiasb5vpmaounyilfuxbd3lryvosl4yefqrfahsb2esg46q6tu6y5q
bafkreia6po64b6tfqq73lckadrhpihg2oubaxgqaoushquhcek46y3zumm
bafkreidc4hz6xawirp4wkcrni54yhvhdawdusbrsskzoqf4avemrlxzw7m
bafkreiah44eqfkfaf4eomjq6x2gcg6q44mt2im3dcv6int42k5pjml5k5y
bafkreibyr5kj7pkocaju3o5xzk3gcsxtgqg6nh23gbvtur7cqoskww4yxe
bafkreicvksdnbh3jxytovgy2alghaayzj4kctsvnyc7fg5wpptosnuf2bm
bafkreihshanjznywfxaxc664xcmsnzwqydntrgsxmbnqqjqeeqxecos2w4
bafkreif6imy7ltlghsk6yncrjrsr7wc5toxhborgcb2dwqo234m2rvsybq
bafkreiestiydyoo2rifwpqews5dc62d2adddrpfvqd7k4bsffygb6ifuf4
bafkreidszrmp3v674lf2rypkal2hgr5qb4imevmlqpdpqougb7zghnnkna
bafkreiblqtq4qdsdqt2ph7xsap5cp2myiuqftt7xd5crljlgj2prwlkqsa
bafkreia4wvraun2neos7xpn7byqxo65jbgjfnl5lmkripawmew6gezyuni
bafkreigbyivpq6rzmva4hl6n65ztg6u5u3zo2zpmgzaceqxlqtnpi77dq4
bafkreiaoj5zr5qx5rngntlrdirizrbd273zdamx4uxahdvxxepeii5t7mi
bafkreidycyuvogknbkwsy5ydpfmq5s4tphdpsauojkgq6vojoj62ksbgeq
bafkreiaz6g7xzoum6udnmxkdfcvnpucn53fdewr3nj4nvzawyn6i7hkxhi
bafkreidajpgiercbn7rneed64s4erjjz7zrfex5s7zftg2zb24zgabbl2q
bafkreibhbx3y6tnn7q4gpsous6apnobft5jybvroiepdsmvps2lmycjjxu

$ ipfs pin ls 
QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc recursive
QmUNLLsPACCz1vLxQVkXqqLX5R1X345qqfHbsf67hvA3Nn recursive
QmQ5vhrL7uv6tuoN9KeVBwd4PwfQkXdVVmDLUZuTNxqgvm indirect
QmejvEPop4D7YUadeGqYWmZxHhLc4JBUCzJJHWMzdcMe2y indirect
QmPZ9gcCEpqKTo6aq61g2nXGUhM4iCL3ewB6LDXZCtioEB indirect
QmQy6xmJhrcC5QLboAcGFcAE1tC8CrwDVkrHdEYJkLscrQ indirect
QmU5k7ter3RdjZXu3sHghsga1UQtrztnQxmTL22nPnsu3g indirect
QmQGiYLVAdSHJQKYFRTJZMG4BXBHqKperaZtyKGmCRLmsF indirect
QmYCvbfNbCwFR45HiNP45rwJgvatpiW38D961L5qAhUM5Y indirect

After this PR

$ ipfs init && ipfs refs local 
generating ED25519 keypair...done
peer identity: 12D3KooWA5CGBJrUmcBFB3fNv3aBWme7kwXkft58EK93yKWcm2KM
initializing IPFS node at /home/lidel/tmp/test-refactor-1680267598
bafkreiczsscdsbs7ffqz55asqdf3smv6klcw3gofszvwlyarci47bgf354

$ ipfs pin ls 
QmUNLLsPACCz1vLxQVkXqqLX5R1X345qqfHbsf67hvA3Nn recursive

(the only pin is the CID of an empty directory used as the initial MFS root)