Fix all Windows-specific test failures caused by path handling problems
and EBUSY errors from unclosed SQLite database handles.
Root causes fixed:
1. POSIX path assumptions: replaced hard-coded file:///tmp, /repo, etc.
with pathToFileURL/path.resolve/path.join computed expectations
2. shortenPath() now normalizes backslashes to forward slashes after ~
and respects home directory boundaries
3. HistoryStorage.resetInstance() leaked its Database — added #close()
that finalizes all prepared statements and closes the DB
4. AgentStorage gained the same resetInstance()/#close() pattern
5. SqliteAuthCredentialStore.close() leaked one-off prepared statements
from inline this.#db.prepare() calls — wrapped each in try/finally
6. model-cache.ts used a process-global DB even for custom dbPath —
now opens/closes per-call via withModelCacheDb
7. createAgentSession leaked AuthStorage on construction failure —
added ownsAuthStorage cleanup in catch block
8. MnemopiBackend.removeDbFiles() now truly best-effort (catches errors)
9. TempDir retry window expanded from 4x10ms to 40x25ms
10. TempDir prefix convention: non-@ prefixes created dirs relative to
cwd instead of os.tmpdir() — all test temp dirs now use @ prefix
11. Shell-escaped interpolated paths in bash tool tests
12. git core.autocrlf false in autoresearch test repo init
All 522 previously-failing Windows tests now pass.
git clone --depth 1 --single-branch only fetches the tip of the
requested branch, so any subsequent git checkout <sha> for a non-tip
commit fails with 'reference is not a tree'. The error was caught and
rethrown as 'shallow clone may not contain this commit', but the clone
arguments were never adjusted.
Drop --depth 1 (and --single-branch when no ref is requested) when the
caller supplies options.sha so the desired commit is present in the
local object store. The ref-only path remains shallow.
Fixes#1589
oldschoola