Follow-up to #27356.
## Stack note
This PR changes Codex's internal dynamic-tool shape while leaving
`thread/start` unchanged. App-server therefore converts the existing
per-tool input into explicit functions and namespaces before passing it
to core.
[#27371](https://github.com/openai/codex/pull/27371) updates
`thread/start` to use the same explicit shape and removes this temporary
conversion.
## Why
Dynamic tools repeat namespace metadata on every function. Core should
keep one explicit namespace with its member tools so descriptions and
membership stay consistent across sessions and runtime planning.
## What changed
- Represent dynamic tools as top-level functions or explicit namespaces
in protocol and session state.
- Read old flat rollout metadata and write the canonical hierarchy.
- Flatten namespace members only when registering callable tools.
- Keep `thread/start.dynamicTools` flat for now and normalize it at the
app-server boundary.
New builds can read old rollout metadata. Older builds cannot read newly
written hierarchical metadata.
## Test plan
- `just test -p codex-app-server
thread_start_normalizes_legacy_dynamic_tools_into_model_request`
- `just test -p codex-protocol
session_meta_normalizes_legacy_dynamic_tools`
- `just test -p codex-core
resume_restores_dynamic_tools_from_rollout_with_sqlite_enabled`
- `just test -p codex-core
tool_search_returns_deferred_dynamic_tool_and_routes_follow_up_call`
- `just test -p codex-core code_mode_can_call_hidden_dynamic_tools`
- `just test -p codex-tools`
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