config-as-code: give sweepWatchdog/prReconciliation top-level flags the self-repo manifest override their siblings already have

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Context

Part of #6275. Four sibling fleet-wide background jobs already got a full top-level self-repo
.loopover.yml override under this same epic — a present manifest block on the loopover self-repo's
own manifest (resolveLoopOverSelfRepoFullName) wins outright over the env var, exactly like
OpsManifestOverride/resolveOpsManifestOverride in src/review/ops-wire.ts:

• LOOPOVER_REVIEW_OPS → ops: block (ops-wire.ts)
• LOOPOVER_REVIEW_DRAFT → draftFlow: block (src/services/draft.ts)
• LOOPOVER_PUBLIC_STATS → publicStats: block (src/review/public-stats.ts)
• LOOPOVER_AUTO_FILE_DRIFT_ISSUES → upstreamDriftIssues: block (src/upstream/ruleset.ts)

Two more background jobs of the identical shape — same "iterate the acting-autonomy repo set on a cron
tick" design, same doc-commented sibling relationship to each other and to ops — never got this:

• LOOPOVER_SWEEP_WATCHDOG — isSweepWatchdogEnabled(env), src/review/sweep-watchdog.ts
• LOOPOVER_PR_RECONCILIATION — isPrReconciliationEnabled(env), src/review/pr-reconciliation.ts

Both already have a per-repo FORCE-OFF-ONLY override (review.sweepWatchdog/review.prReconciliation: false, also added under #6275) that lets one already-watched repo exclude itself from the scan. That part
is intentionally asymmetric and is NOT what this issue is about (see Boundaries below). What's missing is
the top-level flag — today isSweepWatchdogEnabled/isPrReconciliationEnabled read only env, with
no way to flip the whole job on or off from .loopover.yml the way ops/draftFlow/publicStats/
upstreamDriftIssues already can.

Requirements

• Add SweepWatchdogManifestOverride/resolveSweepWatchdogManifestOverride to sweep-watchdog.ts and
  PrReconciliationManifestOverride/resolvePrReconciliationManifestOverride to pr-reconciliation.ts,
  each mirroring OpsManifestOverride/resolveOpsManifestOverride (ops-wire.ts) exactly: a
  { present: boolean; enabled: boolean } shape, read off the loopover self-repo's manifest via
  loadRepoFocusManifest(env, resolveLoopOverSelfRepoFullName(env)), a short in-isolate TTL cache (mirror
  the existing 60s OPS_MANIFEST_OVERRIDE_CACHE_TTL_MS pattern), and fail-safe-to-{present:false} on a
  manifest load error (never let a config-read blip silently enable or disable the job).
• Update isSweepWatchdogEnabled/isPrReconciliationEnabled to accept the optional manifest override
  parameter and check it first (if (manifestOverride?.present) return manifestOverride.enabled;),
  falling through to the existing env-var check only when no override is present — same signature shape as
  isOpsEnabled(env, manifestOverride?).
• Add new top-level manifest keys sweepWatchdog: and prReconciliation: to the shared engine package
  (packages/loopover-engine/src/focus-manifest.ts — FocusManifestSweepWatchdogConfig/
  FocusManifestPrReconciliationConfig, parse functions, *ConfigToJson serializers, EMPTY_*_CONFIG
  defaults), mirroring FocusManifestOpsConfig/parseOpsConfig/opsConfigToJson exactly. These are new
  top-level keys, NOT a rename or reuse of the existing review.sweepWatchdog/review.prReconciliation
  per-repo boolean fields — those stay exactly as-is (per-repo force-off), this is an unrelated sibling
  namespace, same relationship ops: (top-level) already has to any per-repo review.* keys.
• Re-export the new types/functions from src/signals/focus-manifest.ts (the app-local shim file), the
  same re-export list opsConfigToJson/FocusManifestOpsConfig already appear in.
• Update every caller of isSweepWatchdogEnabled/isPrReconciliationEnabled to pass the resolved override
  (mirror how ops-wire.ts's own callers — the cron dispatch and any manual-trigger route — already pass
  resolveOpsManifestOverride's result through).
• Document sweepWatchdog:/prReconciliation: in .loopover.yml.example next to ops:/draftFlow:/
  publicStats:/upstreamDriftIssues:.
• No behavior change for any deployment that doesn't add these blocks to the loopover self-repo's
  .loopover.yml — byte-identical until an operator opts in.

Boundaries — what NOT to touch

• Do not change watchedRepos()'s per-repo scan-set selection in either file, and do not fold the
  per-repo review.sweepWatchdog/review.prReconciliation: false override onto
  feature-activation.ts's resolver. Investigate + design config-as-code for ops / sweep_watchdog / pr_reconciliation #4106 (closed, NOT_PLANNED) already investigated exactly that move
  for these two jobs (plus ops) and rejected it: the per-repo scan-set axis already runs through
  settings.autonomy/isAgentConfigured, and letting a repo-writable, lower-trust .loopover.yml widen
  its own inclusion would spend the operator's shared GitHub API budget on the repo's own say-so — a worse
  trust boundary than today's operator-only allowlist. This issue is scoped ONLY to the top-level,
  operator-writable-only (loopover self-repo) fleet-wide switch — it does not reopen Investigate + design config-as-code for ops / sweep_watchdog / pr_reconciliation #4106's question.
• Do not add a true/force-on value to the existing per-repo review.sweepWatchdog/
  review.prReconciliation keys. They stay force-off-only, unchanged.

Deliverables

• SweepWatchdogManifestOverride + resolveSweepWatchdogManifestOverride in sweep-watchdog.ts
• PrReconciliationManifestOverride + resolvePrReconciliationManifestOverride in pr-reconciliation.ts
• sweepWatchdog:/prReconciliation: top-level manifest config types + parse/serialize functions in
  packages/loopover-engine/src/focus-manifest.ts, re-exported from src/signals/focus-manifest.ts
• Call sites updated to resolve and pass the override through
• .loopover.yml.example documents the two new blocks

Test Coverage Requirements

100% branch coverage on both new resolver functions (present+enabled true/false, absent, manifest-load
error → fail-safe), plus the manifest parse/serialize round-trip for both new config types. src/** and
packages/loopover-engine/src/** are both Codecov-measured (this repo mirrors engine-package coverage per
its own root vitest suite) — aim for 99%+ patch on every changed line and branch, including a regression
test asserting a present-but-enabled:false manifest block turns the job off even when the env var is
"true", and vice versa.

Expected Outcome

An operator can turn LOOPOVER_SWEEP_WATCHDOG and LOOPOVER_PR_RECONCILIATION on or off fleet-wide from
the loopover self-repo's .loopover.yml alone, matching ops/draftFlow/publicStats/
upstreamDriftIssues's already-shipped precedent, with the env var remaining as the fallback default when
no override block is present.

Links & Resources

• Pattern to mirror exactly: OpsManifestOverride/resolveOpsManifestOverride/isOpsEnabled in
  src/review/ops-wire.ts, and its manifest-type sibling in packages/loopover-engine/src/focus-manifest.ts
  (FocusManifestOpsConfig, parseOpsConfig, opsConfigToJson, EMPTY_OPS_CONFIG).
• Prior investigation not to reopen: Investigate + design config-as-code for ops / sweep_watchdog / pr_reconciliation #4106 (closed NOT_PLANNED — per-repo scan-set axis for these same two
  jobs, a different question than this issue).
• Epic: epic: migrate fleet-wide feature-toggle env vars to .loopover.yml config-as-code #6275 · Milestone: Self-Host Config Architecture

[linear-code]

JSO-4472