## Summary
This PR is an alternative approach to #4711, but instead of changing our
storage, parses out shell calls in the client and reserializes them on
the fly before we send them out as part of the request.
What this changes:
1. Adds additional serialization logic when the
ApplyPatchToolType::Freeform is in use.
2. Adds a --custom-apply-patch flag to enable this setting on a
session-by-session basis.
This change is delicate, but is not meant to be permanent. It is meant
to be the first step in a migration:
1. (This PR) Add in-flight serialization with config
2. Update model_family default
3. Update serialization logic to store turn outputs in a structured
format, with logic to serialize based on model_family setting.
4. Remove this rewrite in-flight logic.
## Test Plan
- [x] Additional unit tests added
- [x] Integration tests added
- [x] Tested locally
We truncate the output of exec commands to not blow the context window.
However, some cases we weren't doing that. This caused reports of people
with 76% context window left facing `input exceeded context window`
which is weird.
# Tool System Refactor
- Centralizes tool definitions and execution in `core/src/tools/*`:
specs (`spec.rs`), handlers (`handlers/*`), router (`router.rs`),
registry/dispatch (`registry.rs`), and shared context (`context.rs`).
One registry now builds the model-visible tool list and binds handlers.
- Router converts model responses to tool calls; Registry dispatches
with consistent telemetry via `codex-rs/otel` and unified error
handling. Function, Local Shell, MCP, and experimental `unified_exec`
all flow through this path; legacy shell aliases still work.
- Rationale: reduce per‑tool boilerplate, keep spec/handler in sync, and
make adding tools predictable and testable.
Example: `read_file`
- Spec: `core/src/tools/spec.rs` (see `create_read_file_tool`,
registered by `build_specs`).
- Handler: `core/src/tools/handlers/read_file.rs` (absolute `file_path`,
1‑indexed `offset`, `limit`, `L#: ` prefixes, safe truncation).
- E2E test: `core/tests/suite/read_file.rs` validates the tool returns
the requested lines.
## Next steps:
- Decompose `handle_container_exec_with_params`
- Add parallel tool calls
