R2 virtual workspace docs incorrectly describe raw bucket mount instead of Workspace-backed virtual filesystem

[astrobot-houston]

Originally reported by @stainlu in #155.

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Describe the Bug

The documentation across multiple packages (README.md, docs/deploy-cloudflare.md, packages/cli/README.md, packages/runtime/README.md, packages/sdk/README.md) and the JSDoc comments in packages/runtime/src/cloudflare/virtual-sandbox.ts incorrectly describe the Cloudflare R2 integration as a raw R2 bucket mount. In reality, it creates a Workspace-backed virtual filesystem. The deploy guide also provides direct Wrangler upload instructions instead of the correct workspace seeding approach, which could mislead users into an unsupported workflow.

Refs #153.

Expected Behavior

Documentation and source-level JSDoc should accurately describe the R2 virtual workspace as a Workspace-backed virtual filesystem, and the Cloudflare deploy guide should show the correct seeding workflow rather than direct Wrangler upload steps.

Steps to Reproduce

1. Read the Cloudflare deployment guide at docs/deploy-cloudflare.md
2. Follow the R2 setup instructions, which describe a raw R2 bucket mount and direct Wrangler upload workflow
3. Observe that the described behavior does not match the actual Workspace-backed virtual filesystem semantics of the runtime

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Original implementation from #155 by @stainlu

[stainlu]

makes sense. i think this is the same underlying mismatch as #153.

my read is:

• current runtime contract: getVirtualSandbox(env.BUCKET) creates a Workspace fs indexed by DO SQLite, with R2 as blob storage
• docs currently imply: raw R2 object keys are the fs

i would keep the first fix docs-only: remove the wrangler r2 object put flow and say files need to be written/imported through the workspace fs (session.fs / session.shell). if the intended product contract is raw object-store mounting, that feels like a separate explicit API/design, not a silent special case for AGENTS.md.

implementation branch from #155 is here if useful:
https://github.com/stainlu/flue/tree/docs/clarify-r2-virtual-workspace

[FredKSchott]

Fixed by #154 will go out in a bit