fix: refresh after failed mutating exec runs

[ranveersequeira]

Summary

• continue through refresh and validation after a non-zero wrapped command when runExec detects repository mutations
• preserve the wrapped command exit code instead of masking it with stale-validation exit codes
• add regressions for both runExec and agentify exec --fail-on-stale when a failing command edits tracked files

Testing

• node --test test/exec.test.js
• node --test test/main.test.js
• npm test

Fixes #48

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Continue validation when refresh fails without strict mode

This catch block now always returns refresh-error, even when --fail-on-stale is not set, so validateRepo() is skipped for every refresh failure. In the previous flow, non-strict runs continued to validation and still reported stale/unsafe changes after a partial refresh; with this change, those checks are never emitted and session records show validation as not run. Please keep the early return only for strict failure cases and let non-strict runs fall through to validation while preserving the wrapped command's exit code.

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[ranveersequeira]

@codex fix this

[chatgpt-codex-connector]

Summary

• Updated runExec so refresh failures only short-circuit with phase: "refresh-error" in the strict stale-check case (--fail-on-stale with a non-failing wrapped command). Non-strict paths now continue through validateRepo() and preserve the wrapped command’s exit code behavior. src/core/exec.jsL292-L327
• Preserved refresh failure context for non-strict runs by appending the refresh error message into the returned stderr while still returning phase: "complete" with validation results. src/core/exec.jsL330-L338
• Added a regression test that simulates a failing mutating command plus a refresh-time error, and verifies non-strict exec still validates and keeps the command exit code. test/exec.test.jsL154-L192

Testing

• ✅ node --test test/exec.test.js
• ⚠️ node --test test/main.test.js (one unrelated failing test in this environment: runCli doctor reports MemPalace available via AGENTIFY_MEMPALACE_CMD)

Committed on the current branch (46118d1) and created a follow-up PR with title “fix: continue exec validation after non-strict refresh errors”.

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