Per mara's go-ahead on hyperhive#3902 ("getting started is good, but
terminal rendering does not go in there i think"):
Moved 21 top-level docs/*.md files into 7 new topic subdirectories
(existing web-ui/, turn-loop/, swarm/, tools/, crates/ untouched):
getting-started/ setup.md
agent-lifecycle/ agent-hierarchy.md, approvals.md, persistence.md
trust-boundary/ boundary.md, security.md
integrations/ forge.md, matrix.md, github.md, knowledge.md
networking/ gateway.md, network.md, snapshot-store.md
scheduler/ jobq.md, coordinator.md, ci.md, observability.md
process/ conventions.md, gotchas.md, pr-review-gate.md
web-ui/ terminal-rendering.md (moved into the EXISTING dir,
per mara's correction to the original getting-started
guess -- it's UI implementation detail, not onboarding)
The physical layout now matches docs/README.md's own topical headers,
which already amounted to this taxonomy -- see the scoping comment on
the issue for the two findings that motivated this (a genuine
duplication between CLAUDE.md's old "Reading paths" list and
docs/README.md's grouped one, since drifted out of sync with each
other; and the flat layout not matching the grouping we already had).
Fixed every cross-reference this moved across the whole repo (~120
files: docs/ internal links at every depth, Rust doc comments, nix
module option docs, crate READMEs) -- verified two ways: a grep sweep
confirming zero remaining references to any old path, and a script
that resolves every markdown link in docs/**/*.md + CLAUDE.md +
README.md against the filesystem and reports anything that doesn't
exist (zero broken links).
Collapsed CLAUDE.md's "Reading paths" section (the duplicate) down to
a pointer at docs/README.md, now the single index. Rewrote
docs/README.md itself to use the new subdirectory paths and added the
one doc it was missing that CLAUDE.md's old copy had (pr-review-gate.md).
Classified all 22 docs/*.md files first via a haiku subagent (mara's
suggestion) on two axes -- proposed grouping and operator-vs-
implementation focus -- before finalizing the taxonomy; spot-checked
the report and found internal inconsistencies (its classification
table disagreed with its own summary section for a few files), so this
taxonomy is my original proposal + the one correction mara gave
directly, not a blind application of the subagent's table. The
operator-focus data it gathered is still useful for a follow-up
content pass (docs skewing 'mixed' rather than pure operator-facing),
not addressed in this PR -- structure only.
nix fmt clean, both pre-push lints clean.
Replace the try-and-ignore-duplicate-column approach in apply_migrations
with proper schema versioning using a shared schema_versions table.
## mechanism
New function: db::apply_versioned_migrations(conn, subsystem,
legacy_column, migrations). Tracks the applied-migration count in a
schema_versions table (one row per subsystem key). Only migrations past
the stored version run.
Legacy detection: pre-versioning databases have no schema_versions row.
The legacy_column tuple (table, column) identifies a column that exists
only in a fully-migrated legacy database. If present, all known
migrations are skipped. If absent, migrations start from 0.
## stores migrated
- broker: removes bespoke ensure_message_columns / ensure_reminder_columns.
Unified into BROKER_MIGRATIONS (v1-v5). Legacy detector: messages.priority
(added in the last pre-versioning migration).
- approvals: 4 historical migrations (v1-v4). Legacy detector:
approvals.submitter.
- operator_questions: 3 historical migrations (v1-v3). Legacy detector:
operator_questions.target.
- scheduled_prompts: 1 historical migration (v1). Legacy detector:
scheduled_prompts.paused_at_unix.
apply_migrations removed (no callers).
## tests (db.rs)
- fresh_install_runs_all_migrations
- legacy_install_skips_all_migrations
- partial_migration_resumes_from_version
- already_at_latest_is_noop
- multiple_stores_in_same_db
