Orbit: no persistent way to give the agent output-style directives (e.g. CommonMark-safe markdown with blank lines around lists)

**Reported via beta feedback (v0.5.1).**

A user authoring markdown documents with the agent wants a way to give *persistent* directives about how the model formats its output -- and there's no obvious place to set one.

**Concrete motivating case:** the model emits GitHub-flavored markdown that omits blank lines around lists. The user's external markdown editor follows stricter CommonMark rules and won't recognize a list unless it's surrounded by blank lines, so lists render as plain paragraphs. They'd like to say once -- "write CommonMark-compatible markdown, blank line before and after every list" -- and have it stick for the rest of the session/project instead of re-typing it each prompt.

**The ask, generalized:** a persistent user-directive / "custom instructions" mechanism that gets injected into the agent's context -- a place to record house-style rules (list spacing, tone, formatting conventions) so they aren't repeated every turn and don't get dropped as the conversation grows. Today the system prompt is entirely code-defined (`extensions/loom/context.ts`); there's no user-configurable surface that feeds into it.

**Why it matters:** users are producing real deliverables (documents, notebooks, posts) with Orbit, and small formatting mismatches like this quietly break downstream tooling (editors, renderers). A one-time directive surface is low-friction and generalizes well past this single case.

**Possible directions:**
- A project-level instructions file (an `AGENTS.md`-style doc always loaded into context), if one doesn't already exist.
- A "Custom instructions" field in Preferences that's appended to the system prompt.
- As a cheap stopgap independent of the above: nudge the default system prompt to prefer CommonMark-safe markdown (blank lines around lists), which renders correctly under both GFM and strict parsers -- so the common case is right without any user action.

_(Beta tester feedback; details anonymized.)_

The issue names extensions/loom/context.ts; read that entry point first to understand how the system prompt is assembled and where session or project context enters. Compare the existing project and preferences surfaces before choosing a persistence boundary; done means a user directive survives its intended scope and is consistently included in the agent context, including the motivating CommonMark formatting case.

Written by the indexing model from the issue text.