feat: enable cycle estimation and allocation exclusion by default

[not-matthias]

Summary

Graduate --cycle-estimation and --exclude-allocations out of the experimental flag set so both simulation behaviors are enabled for everyone by default.

• Both are now normal (non-experimental) options with default_value_t = true.
• They remain toggleable escape hatches: --cycle-estimation=false / --exclude-allocations=false (or env CODSPEED_CYCLE_ESTIMATION, CODSPEED_EXCLUDE_ALLOCATIONS) disable them.
• Dropped from the Experimental help heading and no longer trigger the experimental-flags warning.
• --experimental-fair-sched is intentionally left untouched (still experimental, default off).

Changes

File	Change
src/cli/shared.rs	Add cycle_estimation / exclude_allocations toggleable bools (default true, require_equals) to ExecAndRunSharedArgs
src/cli/experimental.rs	Remove both from ExperimentalArgs; only experimental_fair_sched remains
src/cli/run/mod.rs, src/cli/exec/mod.rs	Read the new shared fields
src/executor/config.rs	OrchestratorConfig::test() defaults both true

Behavior note

Runner.exclude_allocations in upload metadata now serializes true on every simulation run (previously omitted via skip_serializing_if). This is the intended signal, just always present now.

Verification

• cargo build, cargo fmt --check, cargo clippy --all-targets clean.
• Verified via the built binary: --cycle-estimation, --cycle-estimation=false, and --exclude-allocations=false all parse; help lists both as normal options.
• Pre-existing Unsupported system valgrind-executor test failures are environment-gated (unsupported valgrind host) and unrelated to this change.

[greptile-apps]

Greptile Summary

This PR graduates cycle estimation and allocation exclusion into default-on runner options. The main changes are:

• New shared run and exec flags for cycle estimation and allocation exclusion.
• Hidden deprecated experimental flags with warning output.
• Updated orchestrator defaults for run, exec, and test helpers.
• Updated upload metadata comments for allocation-exclusion serialization.

Confidence Score: 4/5

This is close, but the metadata hash change should be handled before merging.

• Default runs now serialize excludeAllocations: true.
• The upload hash uses the serialized metadata, so normal runs can get a new hash for the same benchmark invocation.
• The metadata version was not changed with that default-path shape change.

Files Needing Attention: src/cli/shared.rs and src/upload/interfaces.rs

Important Files Changed

Filename	Overview
src/cli/shared.rs	Adds default-on shared options for cycle estimation and allocation exclusion.
src/cli/experimental.rs	Keeps the old experimental options hidden and warning-only after graduation.
src/cli/run/mod.rs	Passes the new shared options into the run orchestrator config.
src/cli/exec/mod.rs	Passes the new shared options into the exec orchestrator config.
src/executor/config.rs	Updates test orchestrator defaults to match the new default-on behavior.
src/upload/interfaces.rs	Keeps allocation exclusion skipped when false and updates the serialization comment.

Prompt To Fix All With AI

Fix the following 1 code review issue. Work through them one at a time, proposing concise fixes.

---

### Issue 1 of 1
src/cli/shared.rs:130
**Upload Hash Changes**

Defaulting `exclude_allocations` to `true` still changes upload metadata for normal `run` and `exec` invocations. The value flows into `Runner.exclude_allocations`, which is only skipped when it is `false`, so the default path now serializes `excludeAllocations: true`. Because the upload hash is computed from the serialized metadata and the metadata version is unchanged, the same benchmark invocation can get a different run hash after this release instead of going through an explicit metadata migration. The `--exclude-allocations=false` opt-out keeps the legacy shape, but that does not cover the new default path.

_{Reviews (5): Last reviewed commit: "feat: enable cycle estimation and alloca..." | Re-trigger Greptile}

[codspeed-hq]

Performance comparison unavailable

A heads-up: this makes performance comparison unavailable when comparing benchmarks before and after this change:

• Cycle estimation changes how benchmark performance is calculated. It was enabled on only one side of the comparison (base off → head on), so the values are not directly comparable. View runner releases
• Allocator-time exclusion changes benchmark values by removing allocator time from the measurement. It was enabled on only one side of the comparison (base off → head on), so the values are not directly comparable. View runner releases

---

_{Comparing cod-2950-enable-cycle-estimationexclude-allocators-in-runner-for (d4b65cd) with main (8611106)}

[GuillaumeLagrange]

olgtm, make sure to not merge before we minor release

[greptile-apps]

Upload Hash Changes

Defaulting exclude_allocations to true still changes upload metadata for normal run and exec invocations. The value flows into Runner.exclude_allocations, which is only skipped when it is false, so the default path now serializes excludeAllocations: true. Because the upload hash is computed from the serialized metadata and the metadata version is unchanged, the same benchmark invocation can get a different run hash after this release instead of going through an explicit metadata migration. The --exclude-allocations=false opt-out keeps the legacy shape, but that does not cover the new default path.

Knowledge Base Used: Upload flow

Prompt To Fix With AI

This is a comment left during a code review.
Path: src/cli/shared.rs
Line: 130

Comment:
**Upload Hash Changes**

Defaulting `exclude_allocations` to `true` still changes upload metadata for normal `run` and `exec` invocations. The value flows into `Runner.exclude_allocations`, which is only skipped when it is `false`, so the default path now serializes `excludeAllocations: true`. Because the upload hash is computed from the serialized metadata and the metadata version is unchanged, the same benchmark invocation can get a different run hash after this release instead of going through an explicit metadata migration. The `--exclude-allocations=false` opt-out keeps the legacy shape, but that does not cover the new default path.

**Knowledge Base Used:** [Upload flow](https://app.greptile.com/codspeed/-/custom-context/knowledge-base/codspeedhq/codspeed/-/docs/upload.md)

How can I resolve this? If you propose a fix, please make it concise.