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 makes cycle estimation and allocation exclusion the normal default behavior. The main changes are:

• Adds default-on shared CLI options for run and exec.
• Keeps the old experimental options hidden as deprecated no-ops.
• Wires the new shared options into orchestrator config.
• Updates test defaults and upload metadata comments for the new default.

Confidence Score: 5/5

This looks safe to merge.

• No blocking issues found in the changed code.

Important Files Changed

Filename	Overview
src/cli/shared.rs	Adds default-on shared flags and environment variables for cycle estimation and allocation exclusion.
src/cli/experimental.rs	Keeps the old graduated experimental fields hidden and warns when active deprecated flags are used.
src/cli/run/mod.rs	Uses the new shared fields when building run orchestrator config and updates test defaults.
src/cli/exec/mod.rs	Uses the new shared fields when building exec orchestrator config.
src/executor/config.rs	Updates test orchestrator defaults to match the new default-on behavior.
src/upload/interfaces.rs	Updates the exclude_allocations serialization comment for the new opt-out behavior.

_{Reviews (6): 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

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_{Comparing cod-2950-enable-cycle-estimationexclude-allocators-in-runner-for (aebdbbc) with main (266f658)}

[GuillaumeLagrange]

olgtm, make sure to not merge before we minor release

[not-matthias]

@greptileai review