fix: atomic counter increment + gitignore overhaul (GH#2067)

[steveyegge]

Summary

Fix-merge of PR #2067 (follow-up to GH#2002 counter-mode review by @gm2211), which had merge conflicts with current main.

• Critical race fix: Replace read-increment-write pattern in nextCounterIDTx with atomic UPDATE SET last_id = last_id + 1 to prevent duplicate issue IDs under concurrent transactions (GH#2002)
• .beads/.gitignore overhaul: Reorganized sections, added fork protection warning against negation patterns, added legacy file cleanup patterns (daemon logs, JSONL sync files)
• Lint fixes: Added nolint:gosec annotations for legitimate dynamic path usage across doltserver, migrations, testutil, and scripts
• Error handling: Fixed unchecked logFile.Close(), rows.Close(), and os.RemoveAll returns
• Formatting: Cleaned up const block alignment in dolt.go

Changes from PR #2067 that were already on main (via prior merges) and skipped:

• doltServerConfig signature cleanup (readOnly parameter removal)
• doctor_test.go Platform map alignment
• migration.go trailing newline removal
• gitignore_test.go comment alignment
• doltserver process-group refactoring (setDetachedProcessGroup -> procAttrDetached)
• sysproc_unix.go / sysproc_windows.go (superseded by doltserver_unix.go / doltserver_windows.go)

Closes #2067

Test plan

• go build ./... passes
• go vet ./cmd/bd/ passes
• Counter-mode tests pass (TestCreateIssue_CounterMode, TestCounterMode_SeedsFromExistingIssues, TestCounterMode_NoExistingIssues, etc.)
• CI pipeline validates full test suite

Co-authored-by: gm2211 gm2211@users.noreply.github.com

🤖 Generated with Claude Code

[codecov-commenter]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
4026	1	4025	451

View the full list of 1 ❄️ flaky test(s)

::TestMain

Flake rate in main: 100.00% (Passed 0 times, Failed 9 times)

Stack Traces | 0s run time

WARN: dolt not found in PATH, skipping test server
PASS
coverage: 17.7% of statements
ERROR: test suite modified repo .beads state:
- metadata.json: exists false → true

FAIL	github..../beads/cmd/bd	15.141s

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