Clarify durable overrides and align Codex with hybrid MCP guidance

[wey-gu]

Summary

This PR does two related cleanup passes across the community integrations repo:

• clarifies the durable override policy across integrations: use the host's own instruction files or settings, not edits inside installed plugin caches
• updates Codex to the recommended hybrid setup: plugin for lifecycle guidance, MCP for stronger retrieval and memory writes, nmem as the universal fallback

It also syncs the nested Gemini CLI integration to the latest needed submodule commit.

What changed

• added a contributor-facing override guide in docs/USER_OVERRIDE_GUIDE.md
• updated integration READMEs to document the real override surface for each host
• aligned docs/PLUGIN_DEVELOPMENT_GUIDE.md and the repo README with that policy
• updated Codex package guidance, skills, and example config for the hybrid plugin + MCP setup
• bumped the Codex plugin package to 0.1.5
• updated integrations.json so Codex is described as cli+mcp
• synced the nowledge-mem-gemini-cli submodule pointer

Why

We were telling users not to edit installed plugin files, but that guidance mostly lived in contributor docs or scattered package READMEs. The policy needs to be explicit and consistent:

• installed plugin files are shipped defaults
• durable customization belongs in the host-owned surface
• Codex is no longer best described as skills-only; in practice plugin + MCP gives better initiative and tool use

Notes

• this PR is mostly docs, registry metadata, and package guidance
• there is no new fake cross-host override filename; the design stays host-native on purpose
• transcript save behavior remains honest: hosts without a real transcript importer should keep using handoff/summary paths instead of pretending they support full save-thread

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 5c8ca212-2582-4a9e-a0f6-1c810db8822a

📥 Commits

Reviewing files that changed from the base of the PR and between d40981f and fc762b7.

📒 Files selected for processing (24)

• README.md
• docs/PLUGIN_DEVELOPMENT_GUIDE.md
• docs/USER_OVERRIDE_GUIDE.md
• integrations.json
• nowledge-mem-alma-plugin/README.md
• nowledge-mem-bub-plugin/README.md
• nowledge-mem-claude-code-plugin/README.md
• nowledge-mem-codex-plugin/.codex-plugin/plugin.json
• nowledge-mem-codex-plugin/AGENTS.md
• nowledge-mem-codex-plugin/CHANGELOG.md
• nowledge-mem-codex-plugin/README.md
• nowledge-mem-codex-plugin/codex.config.example.toml
• nowledge-mem-codex-plugin/skills/distill-memory/SKILL.md
• nowledge-mem-codex-plugin/skills/save-thread/SKILL.md
• nowledge-mem-codex-plugin/skills/search-memory/SKILL.md
• nowledge-mem-codex-plugin/skills/working-memory/SKILL.md
• nowledge-mem-copilot-cli-plugin/README.md
• nowledge-mem-cursor-plugin/README.md
• nowledge-mem-droid-plugin/README.md
• nowledge-mem-gemini-cli
• nowledge-mem-hermes/README.md
• nowledge-mem-openclaw-plugin/README.md
• nowledge-mem-opencode-plugin/README.md
• nowledge-mem-pi-package/README.md

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev_078

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[wey-gu]

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