Two adversarial-review fixes on the #840/#1079 takeovers:
1. importCodeFile's empty-file skip returned skipped WITH an error string.
performSync treats skipped-with-error as a parse failure (failedFiles →
applySyncFailureGate), so any repo containing a legitimate empty code
file (__init__.py, barrel stubs) would BLOCK last_commit for 3
consecutive syncs and then live in the ledger as auto-skipped — the
fix recreated #840's spurious-failure complaint one layer up, and the
became-empty branch reported its own successful stale-page deletion as
a failure. The skip now carries no error, matching the content-hash
short-circuit (banked via markCompleted, never ledgered).
2. runPhaseSync passed noExtract: willRunExtractPhase to EVERY sync
target, but the cycle's extract phase (runPhaseExtract →
extractForSlugs) walks brainDir only — slugs synced from other
sources' checkouts are invisible to it, so their link/timeline
extraction was silently dropped forever. Inline extract is now
deduped only for the brainDir target; other targets keep it, matching
standalone 'gbrain sync --source X' behavior. Pinned by a new
cycle.serial test.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Three community-PR takeovers rebased onto master:
- import-file (#840): importCodeFile skips empty (0-byte) code files instead
of writing a page with empty compiled_truth that fails every reindex-code
pass. When a previously-imported file BECOMES empty, the stale page is
deleted (chunks cascade) instead of ghosting in search — mirrors the
markdown importer's empty-content branch.
- cycle (#1079): runPhaseSync now enumerates every registered, non-archived,
sync-enabled source with a local checkout instead of syncing only the
single brainDir-matched source. Preserves the SyncLockBusyError per-source
skip (#1794), keeps the legacy brainDir fallback when no source covers it,
and respects explicit --source scoping (#1503) so a scoped cycle stays
single-source. Single-target result shape is unchanged.
- link-extraction (#1101): ENTITY_REF_RE gains a root-level branch so
[Name](action-tracker.md) resolves to slug 'action-tracker'. The bare
branch requires the .md suffix and excludes '#', '/', ':' so anchors,
non-markdown assets, and URLs don't emit bogus refs; the capture's .md is
stripped in extractEntityRefs and dir is '' (not the filename).
LINK_EXTRACTOR_VERSION_TS bumped so stamped pages re-extract.
Takeover of #840, #1079, #1101 (rebased; flaws named in review fixed).
Co-authored-by: nightlaro <nightlaro@users.noreply.github.com>
Co-authored-by: samvilian <samvilian@users.noreply.github.com>
Co-authored-by: essexcanning <essexcanning@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
