v3.38.6

## Fixes

**#2947 — `DualModeOrchestrator` left every Codex worker's stdin open, causing `codex exec` to hang waiting for EOF.** Both Claude and Codex workers receive their prompt positionally/via a flag — never over stdin — but the pipe was never written to or closed. `claude -p` ignores the unused pipe, but `codex exec` blocks in `resolve_root_prompt` waiting for stdin EOF that never arrives, hanging every real Codex worker until the orchestrator's own multi-minute timeout kills it. Now closes stdin immediately after spawn for both platforms.

**#2920 — Editing a MEMORY.md section's body (same ID, same entry count) served stale cached content instead of refreshing it.** Two related bugs in the intelligence helper's graph/store caching, both keyed on entry *count* instead of *content*: `init()`'s graph-cache-hit gate compared only node count, so a same-ID content edit was invisible to it and `ranked-context.json` never refreshed; `consolidate()`'s persist gate only fired on insight creation or a dedup-driven shrink, so an in-memory content change (e.g. assigning an id to a previously id-less entry) was silently never written back to disk. Added a `storeFingerprint()` helper folding every entry's content into one aggregate value, used to gate the cache hit and to make `consolidate()` always persist.

**#2935 — `.claude-flow/config.json` `resourceThresholds` overrides were silently lost to a stale `daemon-state.json`.** The daemon's stale-state restoration guard only checked the constructor arg (`originalConfig`), not a value set via `config.json` — so an explicit override (e.g. `minFreeMemoryPercent: 0`, a workaround for Darwin's `os.freemem()` undercounting reclaimable memory) kept losing to whatever a `daemon-state.json` from before the override existed had persisted, on every restart. Same bug class as #2661 (`aiWorkersEnabled`), fixed the same way, per-field. Also fixed a secondary diagnostic bug: `readDaemonConfigFromFile()` logged "Daemon config loaded from ..." from inside the constructor before `this.config` existed, so the log call threw inside its own try/catch and never reached `daemon.log` — made "is the config file even being read?" impossible to answer from the log. Does not address this issue's primary Darwin `os.freemem()` memory-gate report — that needs `vm_stat`/`memory_pressure`-based measurement, left for a follow-up.

## CI infrastructure

Fixed a recurring `sharp`/`libvips` "socket hang up" / 503 flake in `npm ci` across CI workflows (confirmed on 8+ unrelated PRs this session) by adding a retry-with-backoff composite action and wiring it into every `npm ci` call site, including the two OS-conditional fallback blocks initially missed.

## Links

- PR: [#2997](https://github.com/ruvnet/ruflo/pull/2997) (#2947)
- PR: [#2998](https://github.com/ruvnet/ruflo/pull/2998) (CI retry infra)
- PR: [#2999](https://github.com/ruvnet/ruflo/pull/2999) (#2920)
- PR: [#3000](https://github.com/ruvnet/ruflo/pull/3000) (#2935)
- PR: [#3001](https://github.com/ruvnet/ruflo/pull/3001) (CI retry follow-up)
- Previous release: [v3.38.5](https://github.com/ruvnet/ruflo/releases/tag/v3.38.5)