chore: land the remaining low-severity items from the whole-project review

Phase 11 of PROJECT_REVIEW_PLAN.md: the themed cleanup pass over every
low-severity finding still open (2.2-2.3, 3.4-3.6, 4.3-4.7, 6.4-6.7,
7.1-7.3, 8.2-8.3, 9.1-9.4, and the under-documented decisions in §10/§11).

Behavioral fixes:
- Reassign duplicate job IDs in a hand-edited jobs.json instead of letting
  two jobs share one runtime, schedule entry, and SeedStats bucket.
- Disambiguate run-log file names that collide within the same second.
- Compute AvgDurationMS as DurationSumMS/TimedRunCount instead of an
  incremental integer mean, so it always matches the seeded-from-logs
  average instead of drifting from truncation error.
- Clean absolute paths in ResolveConfiguredPath so two spellings of the
  same jobs file do not trigger a spurious adoption.
- Report InstallDesktopIcon failures through ErrorOccurred instead of
  discarding them silently.
- Move settingsView's blocking AutostartStatus (PowerShell on Windows) off
  the UI thread.
- Give notify-timing.tsv its own extension so CleanupLogs no longer
  manages it as a run log.
- Replace the settingsView Save handler's second copy of validateConfig's
  rules with a bare parse, letting the Service's own error surface.

Cleanups:
- Delete collectActivity, the dead yaml tags on RunRecord, and the
  logArguments/LogArguments alias.
- Fold the two systemTrayRegistered/mainWindowHidden globals into one
  trayState instance Run owns and threads through Settings and the
  single-instance reveal path.
- Fix stale comments/docs: the frozen window-size restore claim, a
  reference to a renamed recordRun, README's "Pause all" and notification
  wording, the PowerShell quoting note for TESTS.md's coverage command,
  and scripts/test.bat's UTF-8 checkmarks under a non-UTF-8 code page.
- Document the single-instance fallback's consequence and the
  unauthenticated instance-channel port in STANDARDS.md; record the
  config-shim retirement plan in ROADMAP.md.

3.5, 7.3, and 9.4 turned out to already be fixed by earlier phases; no
change needed for those three.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

src/storage/store.go

@@ -19,6 +19,13 @@ type Store struct {
 // PeekKeepRunningInTray reads keep_running_in_tray from gosentry.json for startup
 // decisions that must run before app.Open(). On error it returns the built-in
 // default.
+//
+// Despite the name, this can write: loadOrCreateConfig creates gosentry.json
+// with defaults on first run, the same as OpenStore does moments later when
+// app.Open() parses the now-existing file again. The double parse and the
+// write-on-read are both harmless — the second read just sees the file the
+// first one created — but worth knowing before adding a third startup path
+// that also wants an early look at the config.
 func PeekKeepRunningInTray() bool {
 	paths, err := ResolvePaths()
 	if err != nil {
@@ -207,13 +214,18 @@ func loadOrCreateJobs(path string) ([]domain.Job, error) {
 
 func normalizeJobs(jobs []domain.Job) {
 	next := 1
+	seen := make(map[int]bool, len(jobs))
 	for index := range jobs {
 		job := &jobs[index]
-		if job.ID <= 0 {
-			// IDs are assigned only when absent. Existing IDs stay stable because
-			// History and future log associations use them to identify jobs.
+		if job.ID <= 0 || seen[job.ID] {
+			// IDs are assigned only when absent or already claimed by an earlier job
+			// in this file — a hand-edited jobs.json can carry two entries with the
+			// same ID, which would otherwise share one runtime, one schedule-cache
+			// entry, and one SeedStats bucket. Existing, unique IDs stay stable
+			// because History and future log associations use them to identify jobs.
 			job.ID = next
 		}
+		seen[job.ID] = true
 		if job.ID >= next {
 			next = job.ID + 1
 		}
@@ -241,7 +253,12 @@ func normalizeJobs(jobs []domain.Job) {
 // apply the same rule to a path the user has typed but not yet saved.
 func ResolveConfiguredPath(appDir string, path string) string {
 	if filepath.IsAbs(path) {
-		return path
+		// Cleaned so two spellings of the same file (forward vs. backslashes, a
+		// trailing separator) resolve to the same string. UpdateSettings compares
+		// this against Paths.JobsPath to decide whether the jobs file is changing,
+		// so an uncleaned path here could trigger a spurious adoption against the
+		// file the app is already using.
+		return filepath.Clean(path)
 	}
 	// Relative paths are resolved against the executable directory, not the
 	// process working directory. This matches ResolvePaths and keeps shortcuts,

src/storage/store_test.go

@@ -4,6 +4,7 @@ import (
 	"encoding/json"
 	"os"
 	"path/filepath"
+	"runtime"
 	"strings"
 	"testing"
 
@@ -145,6 +146,50 @@ func TestNormalizeJobsFillsDefaults(t *testing.T) {
 	}
 }
 
+// TestNormalizeJobsReassignsDuplicateIDs pins the fix for a hand-edited
+// jobs.json carrying two entries with the same ID: without reassignment both
+// would share one JobRuntime, one schedule-cache entry, and one SeedStats
+// bucket, so editing or deleting either would silently affect both.
+func TestNormalizeJobsReassignsDuplicateIDs(t *testing.T) {
+	jobs := []domain.Job{
+		{ID: 5, Name: "First"},
+		{ID: 5, Name: "Second"},
+		{ID: 5, Name: "Third"},
+	}
+
+	normalizeJobs(jobs)
+
+	seen := make(map[int]bool, len(jobs))
+	for _, job := range jobs {
+		if seen[job.ID] {
+			t.Fatalf("ID %d assigned to more than one job after normalization: %+v", job.ID, jobs)
+		}
+		seen[job.ID] = true
+	}
+	if jobs[0].ID != 5 {
+		t.Errorf("first occurrence should keep its ID: got %d, want 5", jobs[0].ID)
+	}
+	if jobs[1].ID == 5 || jobs[2].ID == 5 {
+		t.Errorf("later duplicates should be reassigned away from 5: got %d, %d", jobs[1].ID, jobs[2].ID)
+	}
+}
+
+// TestResolveConfiguredPathCleansAbsolutePaths pins the fix for two spellings
+// of the same absolute path (forward vs. backslashes) resolving to different
+// strings: UpdateSettings compares this against Paths.JobsPath as strings to
+// decide whether the jobs file is changing, so an uncleaned path here could
+// trigger a spurious adoption against the file already in use.
+func TestResolveConfiguredPathCleansAbsolutePaths(t *testing.T) {
+	if runtime.GOOS != "windows" {
+		t.Skip("backslash vs. forward-slash spellings of the same path are a Windows-only ambiguity")
+	}
+	got := ResolveConfiguredPath(`C:\app`, "C:/data/jobs.json")
+	want := ResolveConfiguredPath(`C:\app`, `C:\data\jobs.json`)
+	if got != want {
+		t.Errorf("forward-slash and backslash spellings resolved differently: %q vs %q", got, want)
+	}
+}
+
 func TestLoadOrCreateConfigCreatesDefaultsOnFirstRun(t *testing.T) {
 	dir := t.TempDir()
 	paths := Paths{