The schema probe failed CLOSED: a real WAL codegraph.db in a directory the
process cannot write (a read-only checkout, a mount, another user's tree)
made the read-only node:sqlite open throw — SQLite must create `-shm` to
open a WAL database — and isInitialized() reported the project as not
initialized, where main's file-exists check had been right.
The probe now fails OPEN. Once the size gate and the `SQLite format 3\0`
header have passed, the file is a SQLite database; only a SUCCESSFUL
sqlite_master query proving the `nodes` table absent may return false. Any
open/prepare error (locked, busy, cantopen, readonly, disk I/O) returns
true, the pre-existing behaviour for a database we cannot inspect. No error
strings are matched. The per path + mtime + size memo is unchanged, and
schema-less/empty files still return false, so `codegraph init` still
repairs them and never touches a real db.
Test: a WAL db copied into a `.codegraph/` made read-only with chmod stays
initialized — skipped on win32 and when running as root (root ignores mode
bits).
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
isInitialized() accepted any existing .codegraph/codegraph.db, so an empty or
table-less file in an ancestor directory (an interrupted init, a stray touch,
a never-populated ~/.codegraph/) captured the upward walk of
findNearestCodeGraphRoot / resolveProjectPath / resolveServerRoot for every
project beneath it: the real index of a sub-project became unreachable, the
sub-project down-scan never ran, and commands either operated on the broken
file or failed opening it instead of showing the not-initialized guidance.
An initialized project is now one whose db carries the schema: the probe is
gated by file size (>= the 100-byte SQLite header), then the header magic,
then a read-only node:sqlite open with a single sqlite_master lookup for the
`nodes` table, memoized per path + mtime + size so hot callers (the prompt
hook, MCP root resolution on every call) never reopen an unchanged db. The
handle is closed immediately so the probe never holds the db on Windows; a
locked/busy db counts as live.
createDirectory() uses the same predicate, so `codegraph init` in the
directory with the broken file repairs it in place (the schema is applied
with CREATE ... IF NOT EXISTS) instead of refusing with "Already
initialized"; the CLI says what it found. Nothing is deleted automatically.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
