Merge pull request #484 from forecast-bio/release/v0.5.2

Release v0.5.2

Author: maxine-at-forecast

.crosslink/.gitignore

@@ -2,19 +2,10 @@
 agent.json
 .hub-cache/
 .knowledge-cache/
-.cache/
+.external-cache/
 keys/
 integrations/
 
-# Machine-local state
-issues.db
-issues.db-wal
-issues.db-shm
-session.json
-daemon.pid
-daemon.log
-last_test_run
-
 # Machine-local overrides
 hook-config.local.json
 rules.local/

.crosslink/rules/global.md

@@ -46,28 +46,28 @@ Add labels to control CHANGELOG.md section:
 crosslink quick "Fix login validation error on empty email" -p medium -l bug
 
 # Or use create with flags
-crosslink create "Fix login validation error on empty email" -p medium --label bug --work
+crosslink issue create "Fix login validation error on empty email" -p medium --label bug --work
 
 # Multi-part feature → Epic with subissues
-crosslink create "Add user authentication system" -p high --label feature
-crosslink subissue 1 "Add user registration endpoint"
-crosslink subissue 1 "Add login endpoint with JWT tokens"
-crosslink subissue 1 "Add session middleware for protected routes"
+crosslink issue create "Add user authentication system" -p high --label feature
+crosslink issue subissue 1 "Add user registration endpoint"
+crosslink issue subissue 1 "Add login endpoint with JWT tokens"
+crosslink issue subissue 1 "Add session middleware for protected routes"
 
 # Mark what you're working on
 crosslink session work 1
 
 # Add context as you discover things
-crosslink comment 1 "Found existing auth helper in utils/auth.ts" --kind observation
+crosslink issue comment 1 "Found existing auth helper in utils/auth.ts" --kind observation
 
 # Close when done — auto-updates CHANGELOG.md
-crosslink close 1
+crosslink issue close 1
 
 # Skip changelog for internal/refactor work
-crosslink close 1 --no-changelog
+crosslink issue close 1 --no-changelog
 
 # Batch close
-crosslink close-all --no-changelog
+crosslink issue close-all --no-changelog
 
 # Quiet mode for scripting
 crosslink -q create "Fix bug" -p high  # Outputs just the ID number
@@ -136,12 +136,12 @@ This software supports regulated biotech operations. Every issue MUST have a doc
 
 ```bash
 # These are NOT optional. You MUST use --kind on EVERY comment.
-crosslink comment <id> "Approach: using existing auth middleware" --kind plan
-crosslink comment <id> "Chose JWT over sessions — stateless, simpler for API consumers" --kind decision
-crosslink comment <id> "Found legacy endpoint at /api/v1/auth that conflicts" --kind observation
-crosslink comment <id> "Blocked: CI pipeline timeout on integration tests" --kind blocker
-crosslink comment <id> "Resolved: increased CI timeout to 10m, tests pass" --kind resolution
-crosslink comment <id> "Delivered: JWT auth with refresh tokens, all 47 tests passing" --kind result
+crosslink issue comment <id> "Approach: using existing auth middleware" --kind plan
+crosslink issue comment <id> "Chose JWT over sessions — stateless, simpler for API consumers" --kind decision
+crosslink issue comment <id> "Found legacy endpoint at /api/v1/auth that conflicts" --kind observation
+crosslink issue comment <id> "Blocked: CI pipeline timeout on integration tests" --kind blocker
+crosslink issue comment <id> "Resolved: increased CI timeout to 10m, tests pass" --kind resolution
+crosslink issue comment <id> "Delivered: JWT auth with refresh tokens, all 47 tests passing" --kind result
 ```
 
 **If you close an issue that has zero typed comments, you have violated this rule.**

.crosslink/rules/tracking-normal.md

@@ -7,7 +7,7 @@ Create issues before starting work to keep things organized and enable context h
 - Issue titles should be changelog-ready: start with a verb ("Add", "Fix", "Update"), describe the user-visible change.
 - Add labels for changelog categories: `bug`/`fix` → Fixed, `feature`/`enhancement` → Added, `breaking` → Changed, `security` → Security.
 - For multi-part features: create parent issue + subissues. Work one at a time.
-- Add context as you discover things: `crosslink comment <id> "..."`
+- Add context as you discover things: `crosslink issue comment <id> "..."`
 
 ### Labels for Changelog Categories
 - `bug`, `fix` → **Fixed**
@@ -24,21 +24,21 @@ Create issues before starting work to keep things organized and enable context h
 crosslink quick "Fix auth timeout" -p high -l bug
 
 # Or use create with flags
-crosslink create "Add dark mode" -p medium --label feature --work
+crosslink issue create "Add dark mode" -p medium --label feature --work
 
 # Multi-part feature
-crosslink create "Add user auth" -p high --label feature
-crosslink subissue 1 "Add registration endpoint"
-crosslink subissue 1 "Add login endpoint"
+crosslink issue create "Add user auth" -p high --label feature
+crosslink issue subissue 1 "Add registration endpoint"
+crosslink issue subissue 1 "Add login endpoint"
 
 # Track progress
 crosslink session work <id>
-crosslink comment <id> "Found existing helper in utils/" --kind observation
+crosslink issue comment <id> "Found existing helper in utils/" --kind observation
 
 # Close (auto-updates CHANGELOG.md)
-crosslink close <id>
-crosslink close <id> --no-changelog    # Skip changelog for internal work
-crosslink close-all --no-changelog     # Batch close
+crosslink issue close <id>
+crosslink issue close <id> --no-changelog    # Skip changelog for internal work
+crosslink issue close-all --no-changelog     # Batch close
 
 # Quiet mode for scripting
 crosslink -q create "Fix bug" -p high  # Outputs just the ID number
@@ -71,9 +71,9 @@ Every `crosslink comment` MUST include `--kind` to categorize the comment for au
 - `--kind observation` — when you discover something noteworthy
 
 ```bash
-crosslink comment <id> "Will refactor auth module to use middleware pattern" --kind plan
-crosslink comment <id> "Chose middleware over decorator — matches existing patterns" --kind decision
-crosslink comment <id> "Auth module refactored, 12 tests pass" --kind result
+crosslink issue comment <id> "Will refactor auth module to use middleware pattern" --kind plan
+crosslink issue comment <id> "Chose middleware over decorator — matches existing patterns" --kind decision
+crosslink issue comment <id> "Auth module refactored, 12 tests pass" --kind result
 ```
 
 **You cannot omit `--kind`.** Even for brief comments, categorize them. The audit trail depends on it.
@@ -86,16 +86,16 @@ crosslink comment <id> "Auth module refactored, 12 tests pass" --kind result
 
 ### Dependencies
 ```bash
-crosslink block 2 1     # Issue 2 blocked by issue 1
-crosslink ready         # Show unblocked work
+crosslink issue block 2 1     # Issue 2 blocked by issue 1
+crosslink issue ready         # Show unblocked work
 ```
 
 ### Large Implementations (500+ lines)
-1. Create parent issue: `crosslink create "<feature>" -p high`
-2. Break into subissues: `crosslink subissue <id> "<component>"`
+1. Create parent issue: `crosslink issue create "<feature>" -p high`
+2. Break into subissues: `crosslink issue subissue <id> "<component>"`
 3. Work one subissue at a time, close each when done
 
 ### Context Window Management
 When conversation is long or task needs many steps:
-1. Create tracking issue: `crosslink create "Continue: <summary>" -p high`
-2. Add notes: `crosslink comment <id> "<what's done, what's next>"`
+1. Create tracking issue: `crosslink issue create "Continue: <summary>" -p high`
+2. Add notes: `crosslink issue comment <id> "<what's done, what's next>"`

.crosslink/rules/tracking-relaxed.md

@@ -4,8 +4,8 @@ Crosslink issue tracking is available but not required. Use it when it helps.
 
 ```bash
 crosslink quick "title" -p <priority> -l <label>   # Create + label + work
-crosslink list -s open                              # See open issues
-crosslink close <id>                                # Close issue
+crosslink issue list -s open                              # See open issues
+crosslink issue close <id>                                # Close issue
 crosslink session work <id>                         # Mark focus
 crosslink session end --notes "..."                 # Save handoff
 ```

.crosslink/rules/tracking-strict.md

@@ -46,28 +46,28 @@ Add labels to control CHANGELOG.md section:
 crosslink quick "Fix login validation error on empty email" -p medium -l bug
 
 # Or use create with flags
-crosslink create "Fix login validation error on empty email" -p medium --label bug --work
+crosslink issue create "Fix login validation error on empty email" -p medium --label bug --work
 
 # Multi-part feature → Epic with subissues
-crosslink create "Add user authentication system" -p high --label feature
-crosslink subissue 1 "Add user registration endpoint"
-crosslink subissue 1 "Add login endpoint with JWT tokens"
-crosslink subissue 1 "Add session middleware for protected routes"
+crosslink issue create "Add user authentication system" -p high --label feature
+crosslink issue subissue 1 "Add user registration endpoint"
+crosslink issue subissue 1 "Add login endpoint with JWT tokens"
+crosslink issue subissue 1 "Add session middleware for protected routes"
 
 # Mark what you're working on
 crosslink session work 1
 
 # Add context as you discover things
-crosslink comment 1 "Found existing auth helper in utils/auth.ts" --kind observation
+crosslink issue comment 1 "Found existing auth helper in utils/auth.ts" --kind observation
 
 # Close when done — auto-updates CHANGELOG.md
-crosslink close 1
+crosslink issue close 1
 
 # Skip changelog for internal/refactor work
-crosslink close 1 --no-changelog
+crosslink issue close 1 --no-changelog
 
 # Batch close
-crosslink close-all --no-changelog
+crosslink issue close-all --no-changelog
 
 # Quiet mode for scripting
 crosslink -q create "Fix bug" -p high  # Outputs just the ID number
@@ -85,13 +85,13 @@ Your auto-memory directory (`~/.claude/projects/.../memory/`) contains plans, ar
 
 ```bash
 # Example: translating a memory plan into tracked work
-crosslink create "Implement webhook retry system" -p high --label feature
-crosslink comment 1 "Per memory/architecture.md: retry with exponential backoff, max 5 attempts, dead-letter queue after exhaustion. See 'Webhook Reliability' section." --kind plan
-crosslink subissue 1 "Add retry queue with exponential backoff (max 5 attempts)"
-crosslink comment 2 "Backoff schedule: 1s, 5s, 25s, 125s, 625s. Store attempt count in webhook_deliveries table." --kind plan
-crosslink subissue 1 "Add dead-letter queue for exhausted retries"
-crosslink comment 3 "Failed webhooks go to dead_letter_webhooks table with full payload + error history for manual inspection." --kind plan
-crosslink subissue 1 "Add webhook delivery dashboard endpoint"
+crosslink issue create "Implement webhook retry system" -p high --label feature
+crosslink issue comment 1 "Per memory/architecture.md: retry with exponential backoff, max 5 attempts, dead-letter queue after exhaustion. See 'Webhook Reliability' section." --kind plan
+crosslink issue subissue 1 "Add retry queue with exponential backoff (max 5 attempts)"
+crosslink issue comment 2 "Backoff schedule: 1s, 5s, 25s, 125s, 625s. Store attempt count in webhook_deliveries table." --kind plan
+crosslink issue subissue 1 "Add dead-letter queue for exhausted retries"
+crosslink issue comment 3 "Failed webhooks go to dead_letter_webhooks table with full payload + error history for manual inspection." --kind plan
+crosslink issue subissue 1 "Add webhook delivery dashboard endpoint"
 ```
 
 ### When to Create Issues
@@ -167,23 +167,23 @@ You are explicitly forbidden from using any of the following rationalizations to
 ```bash
 # Starting work on a bug fix
 crosslink quick "Fix authentication timeout on slow connections" -p high -l bug
-crosslink comment 1 "Plan: The timeout is hardcoded to 5s in auth_middleware.rs:47. Will make it configurable via AUTH_TIMEOUT_SECS env var with 30s default." --kind plan
+crosslink issue comment 1 "Plan: The timeout is hardcoded to 5s in auth_middleware.rs:47. Will make it configurable via AUTH_TIMEOUT_SECS env var with 30s default." --kind plan
 
 # You discover something while investigating
-crosslink comment 1 "Found that the timeout also affects the health check endpoint, which has its own 10s timeout that masks the auth timeout on slow connections" --kind observation
+crosslink issue comment 1 "Found that the timeout also affects the health check endpoint, which has its own 10s timeout that masks the auth timeout on slow connections" --kind observation
 
 # You make a design choice
-crosslink comment 1 "Decision: Using env var over config file. Rationale: other timeouts in this service use env vars (see DATABASE_TIMEOUT, REDIS_TIMEOUT). Consistency > flexibility here." --kind decision
+crosslink issue comment 1 "Decision: Using env var over config file. Rationale: other timeouts in this service use env vars (see DATABASE_TIMEOUT, REDIS_TIMEOUT). Consistency > flexibility here." --kind decision
 
 # Something blocks you
-crosslink comment 1 "Blocked: The test suite mocks the auth middleware in a way that bypasses the timeout entirely. Need to update test fixtures first." --kind blocker
+crosslink issue comment 1 "Blocked: The test suite mocks the auth middleware in a way that bypasses the timeout entirely. Need to update test fixtures first." --kind blocker
 
 # You resolve it
-crosslink comment 1 "Resolved: Updated test fixtures to use real timeout behavior. Added integration test for slow-connection scenario." --kind resolution
+crosslink issue comment 1 "Resolved: Updated test fixtures to use real timeout behavior. Added integration test for slow-connection scenario." --kind resolution
 
 # Before closing
-crosslink comment 1 "Result: AUTH_TIMEOUT_SECS env var now controls auth timeout (default 30s). Updated 3 test fixtures, added 2 integration tests. All 156 tests pass." --kind result
-crosslink close 1
+crosslink issue comment 1 "Result: AUTH_TIMEOUT_SECS env var now controls auth timeout (default 30s). Updated 3 test fixtures, added 2 integration tests. All 156 tests pass." --kind result
+crosslink issue close 1
 ```
 
 ### Priority Guide
@@ -194,16 +194,16 @@ crosslink close 1
 
 ### Dependencies
 ```bash
-crosslink block 2 1     # Issue 2 blocked by issue 1
-crosslink ready         # Show unblocked work
+crosslink issue block 2 1     # Issue 2 blocked by issue 1
+crosslink issue ready         # Show unblocked work
 ```
 
 ### Large Implementations (500+ lines)
-1. Create parent issue: `crosslink create "<feature>" -p high`
-2. Break into subissues: `crosslink subissue <id> "<component>"`
+1. Create parent issue: `crosslink issue create "<feature>" -p high`
+2. Break into subissues: `crosslink issue subissue <id> "<component>"`
 3. Work one subissue at a time, close each when done
 
 ### Context Window Management
 When conversation is long or task needs many steps:
-1. Create tracking issue: `crosslink create "Continue: <summary>" -p high`
-2. Add notes: `crosslink comment <id> "<what's done, what's next>"`
+1. Create tracking issue: `crosslink issue create "Continue: <summary>" -p high`
+2. Add notes: `crosslink issue comment <id> "<what's done, what's next>"`

.gitignore

@@ -1,4 +1,5 @@
 **/.DS_Store
+**/.ripsed/
 
 /target/
 /crosslink/target/
@@ -28,13 +29,35 @@ crosslink-enterprise/
 OPUS_4_6_SUGGESTIONS.md
 
 # === Crosslink managed (do not edit between markers) ===
-# .crosslink/ — see .crosslink/.gitignore for machine-local state
-# Tracked: hook-config.json, rules/, .gitignore
+# .crosslink/ — machine-local state (never commit)
+.crosslink/issues.db
+.crosslink/issues.db-wal
+.crosslink/issues.db-shm
+.crosslink/agent.json
+.crosslink/session.json
+.crosslink/daemon.pid
+.crosslink/daemon.log
+.crosslink/last_test_run
+.crosslink/keys/
+.crosslink/.hub-cache/
+.crosslink/.knowledge-cache/
+.crosslink/.external-cache/
+.crosslink/.cache/
+.crosslink/hook-config.local.json
+.crosslink/integrations/
+.crosslink/rules.local/
+
+# .crosslink/ — DO track these (project-level policy):
+#   .crosslink/hook-config.json   — shared team configuration
+#   .crosslink/rules/             — project coding standards
+#   .crosslink/.gitignore         — inner gitignore for agent files
 
 # .claude/ — auto-generated by crosslink init (not project source)
-.claude/settings.local.json
 .claude/hooks/
 .claude/commands/
 .claude/mcp/
-# Tracked: .claude/settings.json
+
+# .claude/ — DO track these (if manually configured):
+#   .claude/settings.json         — Claude Code project settings
+#   .claude/settings.local.json is per-developer, ignore separately if needed
 # === End crosslink managed ===