Feat/ctx desktop

.context/ARCHITECTURE-PRINCIPAL.md

@@ -451,47 +451,66 @@ but shape the architecture significantly:
    are skills and others are prompts, and when to use which, is
    tribal knowledge.
 
-## Domain Clustering Comparison (enriched 2026-04-03 via GitNexus)
+## Domain Clustering Comparison (enriched 2026-06-09 via GitNexus)
 
-GitNexus auto-detected 94 functional clusters from the call graph.
+GitNexus auto-detected 100 functional clusters from the call graph
+(index @ 60d8e823; was 94 at the 2026-04-03 enrichment).
 Comparing against the 5 manual DETAILED_DESIGN domain splits:
 
-| Manual Domain | GitNexus Clusters | Match | Notes |
-|---------------|-------------------|-------|-------|
-| Foundation | Format (97%), Sysinfo (82%), Rc (57%), Io (53%) | Partial | Format is extremely cohesive; Rc and Io are looser than expected |
-| Domain | Drift (263 sym, 84%), Session (110, 88%), Memory (91, 61%), Parser (89, 70%), Journal (74, 47%), Trace (59, 68%) | Partial | Drift is the largest cluster — pulls in cli/drift + write/drift. Journal is low cohesion (47%) |
-| MCP | Server (49, 90%) | Yes | Tight, well-bounded cluster |
-| CLI | Root (85, 83%), Initialize (72, 50%), Bootstrap (41, 67%) | Partial | Initialize is low cohesion — it touches too many domains during deployment |
-| Output | Lock (42, 76%), Notify (46, 65%), Watch (39, 57%) | No | GitNexus doesn't group write/* as a cluster; it groups by behavioral coupling instead |
+| Manual Domain | GitNexus Clusters (top) | Match | Notes |
+|---------------|-------------------------|-------|-------|
+| Foundation | Flagbind (170, 93%), Git (111, 93%), Rc (146, 53%), Format (106, 26%), Store (65, 47%) | Partial | Flagbind and Git are extremely cohesive. Format collapsed from 97% to 26% cohesion — its symbols are now dispersed across consumers |
+| Domain | Memory (91, 60%), Trace (80, 68%), Journal (97, 52%), Parser (64, 75%), Add (67, 62%) | Partial | Journal still low cohesion (52%) — site and import pipelines remain two subsystems sharing a name |
+| MCP | Server (103, 78%), Extract (61, 67%) | Yes | Server cluster doubled in size (49 -> 103 symbols) but stays well-bounded |
+| CLI | Pad (243, 74%), Skill (237, 77%), Initialize (89, 47%), Nudge (72, 79%), Audit (149, 68%) | Partial | Pad and Skill are now the two largest clusters in the codebase. Initialize remains the structural low-cohesion deployment orchestrator |
+| Output | (no matching clusters) | No | Unchanged: write/* and err/* are leaves, not communities |
+
+### Coverage Gaps (clusters with no manual domain)
+
+These clusters exist in the call graph but have no section in any
+DETAILED_DESIGN domain file — the codebase outgrew the 2026-04
+architecture map:
+
+- **Hub (118 symbols, 73%)** — `internal/hub` + `cli/hub` server,
+  persistence, admin setup. Entirely new subsystem.
+- **Steering (95, 61%)** — steering files + drift checks + CLI.
+- **Trigger (72, 63%)** — trigger add/list lifecycle.
+- Also absent: kb (editorial pipeline), connection, handover,
+  message, loop, fmt, permission — visible in the bootstrap
+  registration inventory (42 commands vs 34 documented).
+
+⚠ Recommend a `/ctx-architecture` refresh pass before the next
+enrichment: ~8 command families have no manual baseline to enrich.
 
 ### Hidden Coupling (GitNexus groups, manual splits)
 
-- **Drift cluster (263 symbols)** includes symbols from drift/,
-  cli/drift/, write/drift/, and context/load — all tightly coupled
-  through the Detect() -> load.Do() -> report chain. Manual split
-  puts these in 3 different domains.
-- **Pad cluster (200 symbols)** is self-contained — pad, crypto,
-  and store form a tight unit. Manual split disperses these across
-  Foundation (crypto) and Domain (pad).
+- **Pad cluster (243 symbols, 74%)** — still self-contained (pad,
+  crypto, store history) and still dispersed across Foundation
+  (crypto) and Domain in the manual split.
+- **Rc cluster (146 symbols, 53%)** — now pulls in config profile
+  detection and token/window logic; the manual split keeps rc as
+  a small Foundation leaf, but the graph sees it as a mid-size
+  shared service (rc.RC d=1: 34 across 8 modules).
 
 ### Artificial Grouping (GitNexus splits, manual groups)
 
-- **Journal (47% cohesion)** — lowest cohesion cluster. The site
-  pipeline (zensical, CSS, nav links) and the import pipeline
-  (parser, state, execute) have minimal internal coupling. These
-  are effectively two separate subsystems sharing a command name.
-- **Initialize (50% cohesion)** — touches every domain during
-  deployment (templates, hooks, skills, settings, vscode, makefile,
-  gitignore). Low cohesion is structural, not a bug — it's a
-  deployment orchestrator, not a domain.
+- **Journal (52% cohesion)** — unchanged finding: site pipeline
+  and import pipeline have minimal internal coupling.
+- **Initialize (47% cohesion)** — unchanged: deployment
+  orchestrator, low cohesion is structural, not a bug.
+- **Format (26% cohesion)** — new: the format helpers no longer
+  form a community at all; each helper is coupled to its caller,
+  not to sibling helpers. The manual Foundation grouping is an
+  organizational convenience here.
 
 ### Key Insight
 
-The write/* and err/* layers don't form clusters because they have
-no internal coupling — each write package is called by exactly one
-CLI command. GitNexus correctly identifies them as leaves, not
-communities. The manual "Output" domain is an organizational
-convenience, not an architectural boundary.
+Unchanged from 2026-04: write/* and err/* don't form clusters
+because each package is called by exactly one CLI command — they
+are leaves. The new top-level fact is growth-driven: the two
+largest clusters (Pad 243, Skill 237) and the new Hub/Steering/
+Trigger/KB subsystems all post-date the manual architecture pass,
+so the map's blind spots are now bigger than its mismatches.
 
 ## Questions That Would Sharpen This Analysis
 

.context/CHEAT-SHEETS.md

@@ -208,36 +208,52 @@ Common failure modes:
 
 ---
 
-## Execution Flow Index (enriched 2026-04-03 via GitNexus)
-
-_Auto-detected from the call graph. Complements the manually
-written cheat sheets above._
-
-Top cross-community flows (spanning multiple domains):
-
-| Flow | Steps | Entry Point | Key Symbols |
-|------|-------|-------------|-------------|
-| Deploy -> ContextDir | 10 | initialize | DeployTemplates, Do, ContextDir |
-| Deploy -> Symlinks | 10 | initialize | DeployTemplates, Do, Symlinks |
-| Write -> Init | 10 | MCP server | Serve, Init, SafeWriteFile |
-| Write -> Server | 10 | MCP server | Serve, New, Do |
-| Write -> TokenBudget | 10 | MCP server | Serve, TokenBudget, Do |
-| Run -> Init | 10 | CLI commands | Run, Do, Init |
-| Sync -> ContextDir | 10 | sync cmd | Run, Do, ContextDir |
-| Run -> Text | 9 | CLI commands | Run, Do, desc.Text |
-| Run -> URI | 9 | CLI commands | Run, catalog, URI |
-| Run -> NotFoundError | 8 | CLI commands | Run, Do, NotFound |
+## Execution Flow Index (enriched 2026-06-09 via GitNexus)
+
+_Auto-detected from the call graph (203 flows in index @ 60d8e823).
+Complements the manually written cheat sheets above._
+
+Top cross-community flows (spanning multiple domains). Nearly all
+deep flows terminate at desc.Text — text lookup is the universal
+last step of every command:
+
+| Flow | Steps | Entry Point |
+|------|-------|-------------|
+| RunShow -> Text | 10 | internal/cli/journal/core/source/show.go |
+| Run -> Text (journal import) | 9 | internal/cli/journal/cmd/importer/run.go |
+| Run -> Text (checkversion hook) | 9 | internal/cli/system/cmd/checkversion/run.go |
+| Run -> Text (journal site) | 8 | internal/cli/journal/cmd/site/run.go |
+| Run -> Text (checkcontextsize hook) | 8 | internal/cli/system/cmd/checkcontextsize/run.go |
+| Run -> Text (pad merge) | 8 | internal/cli/pad/cmd/merge/run.go |
+| BuildVault -> Text (obsidian export) | 8 | internal/cli/journal/core/obsidian/vault.go |
+| Run -> Text (pad tag) | 8 | internal/cli/pad/cmd/tag/run.go |
+| Run -> Text (context load gate hook) | 7 | internal/cli/system/cmd/contextloadgate/run.go |
+| Run -> Text (setup) | 7 | internal/cli/setup/cmd/root/run.go |
+| Run -> Text (add) | 7 | internal/cli/add/core/run/run.go |
 
 ### Multi-Flow Hotspots
 
-Symbols participating in 3+ flows (high-impact modification points):
+Symbols participating in 3+ flows (high-impact modification
+points), counted via STEP_IN_PROCESS edges:
 
 | Symbol | Flows | Location |
 |--------|-------|----------|
-| desc.Text | 53 | internal/assets/read/desc/desc.go:75 |
-| load.Do | 100+ | internal/context/load/loader.go:34 |
-| SafeWriteFile | 69 callers | internal/io/security.go |
-| rc.ContextDir | 20+ | internal/rc/rc.go |
-| validate.Symlinks | 10+ | internal/validate/path.go |
-| err/context.NotFound | 30+ | internal/err/context/context.go |
-| rc.RC | 15+ | internal/rc/rc.go |
+| desc.Text | 58 | internal/assets/read/desc/desc.go |
+| check.FullPreamble | 40 | internal/cli/system/core/check/full_preamble.go |
+| check.Preamble | 39 | internal/cli/system/core/check/input.go |
+| load.Do | 28 | internal/context/load/loader.go:34 |
+| session.ReadInput | 26 | internal/cli/system/core/session/session.go |
+| err/context.StatFailed | 25 | internal/err/context/context.go |
+| rc.ContextDir | 25 | internal/rc/rc.go |
+| nudge.Paused | 21 | internal/cli/system/core/nudge/pause.go |
+| hub.Unmarshal | 20 | internal/hub/types.go |
+| rc.RC | 20 | internal/rc/rc.go |
+| io.cleanAndValidate | 15 | internal/io/validate.go |
+| io.SafeReadUserFile | 14 | internal/io/security.go |
+| nudge.PauseMarkerPath | 14 | internal/cli/system/core/nudge/pause.go |
+
+New since 2026-04-03: the system-hook preamble pair
+(FullPreamble/Preamble at 40/39 flows) and nudge pause gating
+(21/14 flows) are now top-tier integration points — every hook
+subcommand routes through them. hub.Unmarshal/Name (20/18) mark
+the hub subsystem as a new flow participant.

.context/CONVERGENCE-REPORT.md

@@ -12,7 +12,7 @@ _Generated 2026-04-03 by /ctx-architecture principal_
 | internal/format | 0.80 | 🟡 Solid | All functions cataloged |
 | internal/parse | 0.80 | 🟡 Solid | Small package, fully understood |
 | internal/sanitize | 0.80 | 🟡 Solid | Small package, fully understood |
-| internal/validate | 0.70 | 🟡 Solid | API inferred; source not directly read this run |
+| internal/validate | 0.75 | 🟡 Solid | Enriched 2026-06-09: Symlinks() is a single-caller chokepoint on the context-load path (9 flows) |
 | internal/inspect | 0.75 | 🟡 Solid | API cataloged from survey |
 | internal/flagbind | 0.85 | 🟡 Solid | Pattern and all variants documented |
 | internal/exec/* | 0.80 | 🟡 Solid | All 5 wrappers surveyed |
@@ -39,7 +39,7 @@ _Generated 2026-04-03 by /ctx-architecture principal_
 | internal/write/* | 0.80 | 🟡 Solid | Pattern understood; not all 46 packages individually read |
 | internal/err/* | 0.80 | 🟡 Solid | Pattern understood; not all 35 packages individually read |
 | internal/audit | 0.75 | 🟡 Solid | Purpose understood; individual test files not read |
-| internal/compliance | 0.70 | 🟡 Solid | Purpose understood; tests not read |
+| internal/compliance | 0.75 | 🟡 Solid | Enriched 2026-06-09: 29 checks cataloged across 4 test files; section added to DETAILED_DESIGN-cli.md |
 
 ## By Domain
 
@@ -50,7 +50,7 @@ _Generated 2026-04-03 by /ctx-architecture principal_
 | MCP | 1 (15 sub-pkgs) | 1/1 | 0.90 |
 | CLI | 2 (34 commands) | 0/2 | 0.78 |
 | Output (write, err) | 2 | 0/2 | 0.80 |
-| Quality (audit, compliance) | 2 | 0/2 | 0.73 |
+| Quality (audit, compliance) | 2 | 0/2 | 0.75 |
 
 ## Overall
 
@@ -142,12 +142,17 @@ which sources to trust.
 
 ## Enrichment Summary
 
-_Last enrichment: 2026-04-03 via GitNexus (index: bf42b1f6)_
+_Last enrichment: 2026-06-09 via GitNexus (index @ 60d8e823,
+27,927 symbols, 203 flows; prior enrichment 2026-04-03 @ bf42b1f6)_
 
 | Phase | Items Processed | Key Findings |
 |-------|----------------|--------------|
-| Danger zones | 25 entries | 4 upgraded to CRITICAL (desc.Text, SafeWriteFile, DescKey-YAML, DiscoverPath); 1 new (load.Do) |
-| Extension points | 14 patterns | Session parser (4 registrations), CLI commands (34), MCP tools (11), MCP prompts (5), agent setup (5) |
-| Execution flows | 257 total, 10 indexed | 7 multi-flow hotspots identified (desc.Text at 53 flows is #1) |
-| Clustering | 94 clusters vs 5 manual domains | Journal (47%) and Initialize (50%) are low-cohesion; write/err are leaves, not communities |
-| Shallow modules | 0 enriched | All modules already >= 0.70; no confidence bumps warranted |
+| Danger zones | 26 entries, 9 symbols re-verified | desc.Text d=1 now 940 (was "30+"); SafeWriteFile 95 (was 69); rc.RC new CRITICAL (d=1: 34, 8 modules); DiscoverPath downgraded CRITICAL->HIGH (d=1: 4, single domain); 3 undercount flags (load.Do, Serve, ValidateAndWrite) |
+| Extension points | 14 patterns | CLI commands 34->42, MCP tools 11->15, drift checks 7->12, setup deployers 5->8 (cline, cursor, kiro, opencode); parsers/prompts unchanged (4/5) |
+| Execution flows | 203 total, 11 indexed | 13 multi-flow hotspots; new top-tier: check.FullPreamble (40) and check.Preamble (39) — every hook routes through them |
+| Clustering | 100 clusters vs 5 manual domains | Coverage gaps now dominate mismatches: Hub, Steering, Trigger, kb + ~8 command families have no manual baseline; Format cohesion collapsed 97%->26% |
+| Shallow modules | 2 enriched | validate 0.70->0.75 (single-caller chokepoint), compliance 0.70->0.75 (29 checks cataloged) |
+
+⚠ The codebase has outgrown the 2026-04 architecture baseline
+(19.3k -> 27.9k symbols). Recommend `/ctx-architecture` refresh
+before the next enrichment pass.