BrainPalace 26.6.20

Fixed

• Fresh-folder watch=auto is now persisted at the start of indexing, not only on clean completion. The folder record was written watch=off mid-job and only upgraded to auto at clean completion, so a first index killed mid-tail left a brand-new folder unwatched. An explicit --watch flag now always wins; a flagless re-index still preserves the folder's existing setting.
• Indexing now honours .git/info/exclude and the global core.excludesFile in addition to .gitignore, matching Git's ignore precedence — local-only excludes (including potential secrets) are no longer indexed. info/exclude is located via --git-common-dir so linked worktrees resolve correctly.
• Indexing progress now advances through the whole pipeline instead of sitting at one value and then jumping to 100%. Progress persistence is throttled by percent-of-total, percent bands are rebalanced, and the graph-build phase reports per-document progress.
• langextract not installed is logged once per process instead of once per document.
• Project discovery now ignores an uninitialized .brainpalace/ scaffold. A stray .brainpalace/ with no config.json/config.yaml/runtime.json was mistaken for a project root, causing phantom nested projects and double-indexing.

Changed

• brainpalace status splits documents and chunks into code vs doc counts (N (X code · Y docs)). The split survives a server restart without a reindex.
• brainpalace status always shows session summarization as its own row, even when off — clarifying that summarization (free) is independent of session embedding (billable) and raw archive.

Deprecated

• BRAINPALACE_CHECKPOINT_INTERVAL / progress_checkpoint_interval no longer affect indexing-progress cadence. Progress is now percent-based (PROGRESS_MIN_PERCENT); the legacy setting is accepted but ignored.