What 1,000+ Codex CLI issues reveal about AI dev tools that teams actually use

We analyzed 1,000+ issues in the Codex command-line interface (CLI) repository and surfaced 10 themes that repeatedly block adoption or unlock delight. These lessons generalize to every AI coding tool and agentic CLI.

Here’s the punchline:

• Teams don’t just want more model power.
• They need predictable guardrails and smoother multi-day sessions.
• Trustworthy long-task UX matters.
• First-class automation hooks are non-negotiable. In short: operational excellence beats raw IQ.

Methodology: We used Agyn Deep Researchers to analyze 1,000+ Codex CLI issues, group them by themes, and synthesize the write-up. For each theme, we surfaced the top relevant issues that best illustrate developer needs.

Quick overview

• Approvals and policy controls
• Sessions: resume, naming, branching
• Long tasks and execution experience
• Model Context Protocol (MCP) ecosystem: tools and lifecycle
• Custom prompts and reusable commands
• Context window management and compaction
• Cost, limits, and usage visibility
• Editor and input power-user UX
• SDK, headless, and automation
• Plan mode and explainability

1. Approvals and policy controls

Problem: Teams want to move fast, but not hand over full control. Today, working with AI agents means either clicking “yes” a hundred times or giving blanket access that feels risky. From issue #4665:

Codex needs a smarter way to handle approvals. I've had to spend way too long repeatedly approving requests to add and commit changes to git.

2. Sessions: resume, naming, branching

Problem: Work happens over days, not minutes. If you can’t instantly pick up where you left off—or branch an idea without losing the main thread—flow breaks and time is wasted. From issue #4545:

I’m requesting a way to resume the most recent Codex session scoped to the current directory/workspace, not the global last session. In #4342, I was advised to use codex resume --last, but that resumes the global latest session across all directories on the machine.

3. Long tasks and execution experience

Problem: Long runs shouldn’t be black boxes. Engineers need clear progress, trustworthy completion signals, and correct exit codes so they don’t babysit jobs. From issue #4751:

I would like the ability to see the real-time stdout and stderr from long-running shell commands that Codex executes, especially those run via MCP tools. Currently, when Codex runs a command like npm run test:e2e or a large npm install, the TUI only displays a generic spinner (e.g., ⠏ Running npm run test:e2e).

4. Model Context Protocol (MCP) ecosystem: tools and lifecycle

Problem: Connecting internal tools should be boring. Project-scoped MCP configs and reliable lifecycle controls prevent flaky setups and “works on my machine” churn. From issue #5059:

It is so common that MCP servers provide some prebuilt prompts to assist users with their requests. Currently Codex only supports MCP's tools but it would be great having it available for the next step, so users can simply get the a prompt by typing "/".

5. Custom prompts and reusable commands

Problem: Teams repeat the same flows all day. Make them one-click: reusable prompts/commands that everyone can find, trust, and version. From issue #4209:

I'd like to request a new feature for Codex CLI: a built-in /prompt command to manage reusable custom prompts.

6. Context window management and compaction

Problem: Token limits are real. Give predictable compaction and safe auto-continue so work keeps moving without surprise cut-offs. From issue #4924:

After using the tool for a short while, the conversation is unable to continue, with the error Codex ran out of room in the model's context window. Start a new conversation or clear earlier history before retrying. Similar to the CLI tool, the chat should be condensed and summarised to free up space and allow the conversation to continue.

7. Cost, limits, and usage visibility

Problem: Costs and rate limits shouldn’t ambush you mid-task. Show limits up front and warn early so runs don’t stall. From issue #4685:

The old JSON format printed out rate limit information periodically, but the new format does not. It would be great to have this back.

8. Editor and input power-user UX

Problem: The CLI is where devs live. Fast text editing and shortcut discoverability keep muscle memory intact and errors down. From issue #3049:

It would be highly valuable to introduce configurable hotkeys in Codex. Currently, key bindings such as Ctrl+J, Ctrl+H, etc., are hardcoded.

9. SDK, headless, and automation

Problem: Automation is table stakes. Provide headless, scriptable flows that run the same locally and in CI—no TUI required. From issue #2772:

Introduce a Codex SDK (TypeScript and Python) that programmatically drives the existing codex CLI in a headless, JSON-event-stream mode. The SDK would expose the same tools, permissions, and MCP capabilities as the CLI, plus structured streaming for integration with IDEs, agents, CI/CD, and server apps.

10. Plan mode and explainability

Problem: Before acting, agree on a plan. A read-only planning step makes changes predictable, reviewable, and easy to adjust. From issue #4897:

I would like to propose the addition of a "Plan Mode" to the codex-cli. This mode would be designed to handle complex, multi-step coding tasks by first generating a comprehensive implementation plan for user review before any code is modified or commands are executed.

Full Report

Theme	Description	Why it's important	User pain	Win if delivered	Representative issues
Approvals and Policy Controls	Granular, predictable approvals and policy management for commands, files, and tools (per-command whitelists, read vs write policy, profiles, org/user policy center).	Developers need to move fast without unsafe blanket approvals; teams need guardrails that are clear, auditable, and easy to tune.	Too many prompts or all-or-nothing trust causes either friction or unsafe actions; orgs can't centrally express rules.	Low-friction flows with the right approvals auto-granted; safer defaults; team-wide policies that 'just work.'
Sessions: Resume, Naming, Branching	Make sessions first-class: resume reliably, name/alias sessions, fork/branch from prior steps, and keep cwd/context sane.	Coders often juggle tasks over days; returning to the right state is critical to continuity and collaboration.	Losing the trail or wrong cwd breaks flow; can't easily branch ideas or organize by human-friendly names.	Fast re-entry into the exact spot; clean branching for experiments; less context rework.
Long tasks and Exec UX	Better control and feedback for long-running commands: live streaming, default timeouts, proper exit codes, toggle streaming, safe re-send, and explainability hooks.	Execution is where time is lost; poor feedback or hanging jobs force babysitting or re-runs.	Stuck or silent runs, no clear signal when done, brittle interrupts, and accidental double-sends.	Trustworthy, smooth runs: see progress live, interrupts behave, you can safely retry, and get signals on completion.
MCP ecosystem: tools and lifecycle	Richer MCP client features and lifecycle controls: prompts support, restart servers, expose resources, sampling, project-scoped servers, image responses, and cloud support.	MCP is how teams wire internal systems; operability and ergonomics decide real adoption.	Flaky servers, no restart knobs, missing resource access, and poor discovery slow teams.	A dependable platform: servers are manageable, resources available, and features feel native to Codex.
Custom prompts and reusable commands	First-class support for creating, organizing, and invoking reusable prompts and commands across projects.	Teams repeat patterns; codifying them boosts consistency and speed.	Copy-paste templates go stale; discoverability and versioning are ad hoc.	A small shared library of prompts/commands becomes a superpower for the team.
Context window management and compaction	Explicit controls and displays for token budget: manual /compact, show remaining, auto-compact and auto-continue modes, and ability to turn policies on/off.	Long diffs and conversations routinely exceed model limits; users need predictable tools to manage it.	Runs die mid-way; users prune context by hand and lose momentum.	Work continues smoothly: Codex compacts and continues automatically, with controls when you need them.
Cost, limits, and usage visibility	Surface cost/usage clearly and provide smart fallbacks: rate limit metadata, stats toggles, and automatic switch to API credits when Plus runs out.	Developers need to manage spend and avoid session-killing limits.	Unexpected caps stall work; no easy way to see or route around limits.	Clear heads-up on usage, and seamless fallback keeps work moving without surprises.
Editor and input power-user UX	Powerful, predictable TUI editing: configurable hotkeys, minimal line editor commands, Vim-like editing, platform-specific hints, file path visibility.	The CLI is a daily driver; text ergonomics compound every minute.	Basic edits feel slow or unfamiliar; muscle memory breaks, and context (like full paths) is missing.	Typing feels native; fewer keystrokes, fewer mistakes; users stay in flow.
SDK, headless and automation	Programmatic control and non-interactive auth: official SDKs, headless login, event hooks, and custom auth flows.	Teams want to integrate Codex into CI, bots, and bespoke tooling.	Lack of APIs and headless auth forces brittle scraping or manual steps.	A clean SDK + headless auth unlocks automation safely and at scale.
Plan Mode and explainability	Upfront plan-first workflows and transparency controls: explicit Plan Mode, model/effort cycling, and ongoing-thoughts display.	Complex tasks benefit from planning and user oversight; reduces rework and surprises.	Agents jump into doing without a shared plan; hard to steer or audit mid-flight.	Codex agrees on a plan, shows its thinking at the right fidelity, and remains steerable.

How agyn helps

In agyn, we’ve invested heavily in observability, approvals, and session continuity so teams can ship agentic workflows with confidence. If you’re building AI dev tools and want pragmatic patterns (and pitfalls to avoid), reach out—we’re happy to share what’s worked.