/{cmd,internal}: get dolt backend init working and allow issue creation

P0 #1: Conflict detection now happens BEFORE push to prevent data loss.
Previously: Pull -> Push -> Detect conflicts (wrong - conflicts overwritten)
Now: Pull -> Detect conflicts -> Push (skip conflicting issues)

P0 #2: Added SyncContext struct for thread-safe sync operations.
- SyncContext holds store, actor, dbPath, issueIDCounter
- WithContext variants of all sync functions
- globalContextIDCounter for cross-context uniqueness
- Enables concurrent sync operations without race conditions

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Executed-By: beads/crew/emma
Rig: beads
Role: crew

Add atomic transaction counter to track active transactions and ensure
reconnect() waits for in-flight transactions to complete. This prevents
data loss when the database file is replaced during an active write.

Security fixes from SECURITY_AUDIT.md:
- Issue #2: Reconnect closing connection while transaction is active
- Issue #5: Daemon crash leaving stale lock files

Changes:
- Add activeTxCount atomic counter to SQLiteStorage struct
- Update RunInTransaction to increment/decrement counter
- Update reconnect() to wait for active transactions with timeout
- Add exponential backoff retry for BEGIN IMMEDIATE
- Improve daemon lock file cleanup on normal shutdown
- Add flock-based stale lock detection

Comprehensive race condition tests:
- store_race_test.go: SQLite store concurrency
- daemon_lock_race_test.go: Daemon lifecycle and lock handling

Co-Authored-By: SageOx <ox@sageox.ai>

…ect support

Addresses review item #2: _find_beads_project duplicated the upward
directory walk but skipped .beads/redirect handling. Now delegates to
_find_beads_db_in_tree, inheriting redirect, symlink, and all backend
detection for free.

Amp-Thread-ID: https://ampcode.com/threads/T-019d84e2-3a96-7263-a399-c3b2cc0ba6bb
Co-authored-by: Amp <amp@ampcode.com>

gastownhall#3207)

* fix(mcp): detect Dolt-backed projects in workspace discovery (GH#2997)

The MCP `context()` tool reported "Database: Not found" for embedded Dolt
projects because `_find_beads_db()` and `_find_beads_db_in_tree()` only
globbed for `*.db` files. Embedded Dolt projects keep their data under
`.beads/embeddeddolt/` and declare the backend in `.beads/metadata.json`
— there is no `*.db` file to find.

Adds `_has_beads_project_files()` mirroring Go's `hasBeadsProjectFiles`
(metadata.json, config.yaml, dolt/, embeddeddolt/, or non-backup *.db).
Both Python discovery functions (and `.beads/redirect` validation) now
use this check, so SQLite, embedded Dolt, and server Dolt projects are
all recognized.

`context()` now reports the project root and backend when no SQLite db
is present, instead of the misleading "Not found".

* fix: delegate _find_beads_project to _find_beads_db_in_tree for redirect support

Addresses review item #2: _find_beads_project duplicated the upward
directory walk but skipped .beads/redirect handling. Now delegates to
_find_beads_db_in_tree, inheriting redirect, symlink, and all backend
detection for free.

Amp-Thread-ID: https://ampcode.com/threads/T-019d84e2-3a96-7263-a399-c3b2cc0ba6bb
Co-authored-by: Amp <amp@ampcode.com>

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Co-authored-by: Amp <amp@ampcode.com>