I'm running Spigot-1.8.8 on my self-hosted server with OpenJDK 8. It seems PEX2 keeps malfunction and all commands are denied.

pex user amamoyou perm * 1
[19:25:15 INFO]: Set permission =1 for user 78899abd-6be6-3ad3-94c4-427918c1c457/amamoyou in Global context
pex user amamoyou perm *. 1
[19:25:17 INFO]: Set permission .=1 for user 78899abd-6be6-3ad3-94c4-427918c1c457/amamoyou in Global context
pex user amamoyou perm essentials.gamemode 1
[19:25:26 INFO]: Set permission essentials.gamemode=1 for user 78899abd-6be6-3ad3-94c4-427918c1c457/amamoyou in Global context
[19:25:31 INFO]: UUID of player amamoyou is 78899abd-6be6-3ad3-94c4-427918c1c457
[19:25:31 INFO]: amamoyou[/125.122.42.184:49962] logged in with entity id 211 at ([world]-24.753082962277524, 64.0, 226.80945094798378)
[19:25:34 INFO]: amamoyou issued server command: /gm 1
[19:25:34 INFO]: §camamoyou §4was denied access to command.
[19:26:20 INFO]: amamoyou issued server command: /pex user amamoyou perm * 1

the client shows:
"You do not have permission to use this command"

User "amamoyou" is already opped. Permissions are correctly written into "permissions.json" as I checked.
Is it regarding version compatibility or something else?

when you first set up you need to at least manually edit the permissions.yml to add you as admin so you can have rights to do add perms, groups, etc.

groups:
default:
options:
default: true
permissions:
- modifyworld.*
Admin:
- permissions.setrank.*
- permissions.*
schema-version: 1
users:
00f01363-7d82-47c2-8d4c-98d7180hytee:
group:
- Owner
options:
name:

@Ironic8b498 no, that's PEX1 -- PEX2 does not use a permissions.yml

For PEX2, the * node is not used at all. Instead, giving a node implies giving that node with .* appended. For a root *, a default permission can be set with /pex group <group> def true