test: remove fixed tests from fragile lists

Checked and found that:

  #4353 -> tarantool/tarantool-qa#13:
    engine/ddl.test.lua fixed in #6102.
  #4926, tarantool/tarantool#115:
    box/alter_limits.test.lua fixed in
    tarantool/tarantool-qa#126.
  #5547 -> tarantool/tarantool-qa#50:
    box/net.box_schema_change_gh-2666.test.lua fixed in
    tarantool/tarantool-qa#126.
  #5583 -> tarantool/tarantool-qa#22:
    box/net.box_methods_gh-3107.test.lua fixed in
    tarantool/tarantool-qa#126.

Closes tarantool/tarantool-qa#13
Closes tarantool/tarantool-qa#115
Closes #4926
Closes tarantool/tarantool-qa#50
Closes tarantool/tarantool-qa#22

test/box/suite.ini

@@ -29,9 +29,6 @@ fragile = {
         "tree_pk.test.lua": {
             "issues": [ "gh-4882" ]
         },
-        "alter_limits.test.lua": {
-            "issues": [ "gh-4926" ]
-        },
         "misc.test.lua": {
             "issues": [ "gh-4982" ],
             "checksums": [ "851dcc5dfd0cc77456ce1d9e6ec7d38f" ]
@@ -161,10 +158,6 @@ fragile = {
             "issues": [ "gh-5546" ],
             "checksums": [ "6379f11bde87b463059911b670a29906" ]
         },
-        "net.box_schema_change_gh-2666.test.lua": {
-            "issues": [ "gh-5547" ],
-            "checksums": [ "193c3e139deb808a93f8f62a7ce96d28" ]
-        },
         "net.box_iproto_hangs_gh-3464.test.lua": {
             "issues": [ "gh-5548" ],
             "checksums": [ "78e53d88a92708766af55557fc5889b2" ]
@@ -268,10 +261,6 @@ fragile = {
         "tx_man.test.lua": {
             "issues": [ "gh-5579" ],
             "checksums": [ "72a91771dd0a3e4a1a4052f61e4b72e9" ]
-        },
-        "net.box_methods_gh-3107.test.lua": {
-            "issues": [ "gh-5583" ],
-            "checksums": [ "9e5c778bd463ac88d2d51e428c9de427" ]
         }
     }
   }

test/engine/suite.ini

@@ -12,10 +12,6 @@ is_parallel = True
 fragile = {
     "retries": 10,
     "tests": {
-        "ddl.test.lua": {
-            "issues": [ "gh-4353" ],
-            "checksums": [ "c04fa9a0fae1bb63a86a5304f7679245", "f2e895cb6be3cd2d1c059b9c4b35e256", "0498012b878a6c638687a0b5de6e2090", "fc6d3bcd8d2d745d9dd34245b18186f1", "d54ee830446114bbe9d8fec8ac68be90" ]
-        },
         "gh-4973-concurrent-alter-fails.test.lua": {
             "issues": [ "gh-5157" ],
             "checksums": [ "4e797e63335cebe24dab15eae4aa8044" ]