fix: honor deprecated experimental flags instead of ignoring them

[not-matthias]

--experimental-cycle-estimation and --experimental-exclude-allocations were parsed but deliberately dropped. Since --exclude-allocations defaults to false, anyone still passing the old flag silently lost allocation exclusion.

Both now feed their graduated counterparts, and the warning states the truth instead of "has no effect":

⚠ --experimental-exclude-allocations is deprecated and will be removed in a future release: use --exclude-allocations instead.

Closes COD-3511

[greptile-apps]

Confidence Score: 4/5

The PR is not yet safe to merge because its deprecation warnings are silently discarded for the Run and Exec commands.

Findings

1.  Deprecation warnings are suppressed ▶

Fix with agent prompt

### Issue 1
src/cli/experimental.rs:92-94
For `run` and `exec`, `warn_if_deprecated()` runs before those commands initialize their logger. As a result, `log::warn!` uses the no-op logger, so users who pass either deprecated flag do not see the promised migration warning. Keep this warning on a pre-initialization output path or emit it after logger setup.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

Summary

This PR makes deprecated cycle-estimation and allocation-exclusion flags feed their stable counterparts for both run and exec.

• Adds shared resolution helpers that combine stable and deprecated options.
• Uses the resolved values when constructing orchestrator configurations.
• Revises deprecation messaging to recommend the stable flags.
• The latest warning implementation runs before logger initialization and is therefore suppressed on the affected commands.

_{Reviews (2) · Last reviewed commit: "fix: honor deprecated experimental flags..."}

[codspeed]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 17 untouched benchmarks

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_{Comparing fix/deprecated-experimental-flags (e11c9df) with main (37eba9e)}

[greptile-apps]

Deprecation warnings are suppressed

For run and exec, warn_if_deprecated() runs before those commands initialize their logger. As a result, log::warn! uses the no-op logger, so users who pass either deprecated flag do not see the promised migration warning. Keep this warning on a pre-initialization output path or emit it after logger setup.

Prompt To Fix With AI

This is a comment left during a code review.
Path: src/cli/experimental.rs
Line: 92-94

Comment:
**Deprecation warnings are suppressed**

For `run` and `exec`, `warn_if_deprecated()` runs before those commands initialize their logger. As a result, `log::warn!` uses the no-op logger, so users who pass either deprecated flag do not see the promised migration warning. Keep this warning on a pre-initialization output path or emit it after logger setup.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.