Rewrite every docs/ reference and integration guide example that
previously showed legacy flat TOML (`[llm]`, `[vars]`, `[sandbox]`,
`[setup]`, `[exec]`, `[fabro]`, `[pull_request]`, `[mcp_servers]`,
`[git]`, `[web]`, `[api]`, `[features] retros`, `version = 1`,
top-level `storage_dir`) to use the v2 namespaced schema. Also update
the surrounding prose to describe v2 merge semantics (R22 run.inputs
wholesale replacement, R71 sticky sandbox.env/labels, R30 whole-list
prepare.steps replacement, hook id-based replacement).
Files touched:
- docs/reference/user-configuration.mdx (complete rewrite around
[cli.*] ownership, [run.*] run-scoped defaults, [cli.target] /
[cli.exec] / [cli.output] / [cli.updates] / [cli.logging], and
[run.agent.mcps.<name>] with durations like "10s")
- docs/reference/cli.mdx (settings.toml example uses [cli.exec.*],
[run.model], [cli.target])
- docs/execution/run-configuration.mdx (full run-config example
rewritten to use [workflow].graph, [run].goal/working_dir,
[run.model], [run.prepare.steps], [run.sandbox.daytona.snapshot]
with Size values, [run.inputs], [run.artifacts], [run.agent.mcps],
[run.pull_request], [[run.hooks]] with optional id and duration
timeout; section docs explain the new merge semantics)
- docs/execution/environments.mdx and devcontainers.mdx (sandbox
examples now use [run.sandbox.*])
- docs/execution/retros.mdx (retros moved to [run.execution] retros
= true per R31)
- docs/execution/failures.mdx (fallbacks now a single ordered array
under [run.model].fallbacks)
- docs/workflows/variables.mdx ([vars] → [run.inputs], wholesale
replacement semantics explained)
- docs/administration/server-configuration.mdx (full reference
rewritten around [server.listen]/[server.api]/[server.web]/
[server.auth]/[server.storage]/[server.scheduler]/[server.logging]/
[server.integrations])
- docs/api-reference/overview.mdx (auth strategies now enabled via
[server.auth.api.jwt].enabled and [server.auth.api.mtls].enabled;
listener TLS moved to [server.listen.tls])
- docs/integrations/daytona.mdx, github.mdx (provider config now
nested under [run.sandbox.daytona] / [server.integrations.github])
- docs/human-tools/ssh-access.mdx (sandbox examples to v2)
- docs/agents/mcp.mdx (Playwright sandbox example to [run.agent.mcps])
- docs/core-concepts/models.mdx (model config and fallbacks array to
[run.model])
Canonical fabro-cli overrides and server run_manifest now emit
verbose via [cli.output].verbosity = verbose rather than the prior
run.metadata staging. No code changes beyond those Stage 4 fixes that
were already in flight.
Consolidate CLI and server machine defaults under settings.toml,
including loader renames, writer preservation fixes, same-machine
manifest handling, and docs/test updates for the new config model.
Move secret storage, diagnostics, and repo/provider validation behind the
server API so credentials live under the server storage dir and take effect
immediately without process env mutation.
This also removes the old .env runtime path, rewires doctor/install/secret/
provider login/repo init around the server contract, and regenerates the
TypeScript client for the new endpoints.
