refactor: rename .scripts/ → cli/

The TypeScript tooling (2K+ files, 900+ tests, full CLI application)
has outgrown the "scripts" name. Renamed to cli/ to honestly reflect
what it is.

All internal references updated. No import path changes needed.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: aRustyDev

.claude/plans/.archive/agents-tool-improvement/phase/1-error-log-separation.md

@@ -27,10 +27,10 @@ Separate error records from the catalog into an append-only error log file. Cata
 
 | Deliverable | Location | Format |
 |-------------|----------|--------|
-| Error log types + functions | `.scripts/lib/catalog.ts` | TypeScript |
-| Updated merge function | `.scripts/lib/catalog.ts` | TypeScript |
-| Updated errors CLI | `.scripts/commands/skill.ts` | TypeScript |
-| Error log tests | `.scripts/test/catalog-tier1.test.ts` | TypeScript |
+| Error log types + functions | `cli/lib/catalog.ts` | TypeScript |
+| Updated merge function | `cli/lib/catalog.ts` | TypeScript |
+| Updated errors CLI | `cli/commands/skill.ts` | TypeScript |
+| Error log tests | `cli/test/catalog-tier1.test.ts` | TypeScript |
 | Gitignore update | `context/skills/.gitignore` | Text |
 
 ## Files
@@ -39,9 +39,9 @@ Separate error records from the catalog into an append-only error log file. Cata
 - None (error log file created at runtime)
 
 **Modify:**
-- `.scripts/lib/catalog.ts` — `ErrorRecord` type, error log functions, update `Tier1Result`, update `mergeTier1Results` signature and implementation
-- `.scripts/commands/skill.ts` — update `processBatch` to pass `errorLogPath` to merge, update `catalog errors` subcommand, add `--prune` flag
-- `.scripts/test/catalog-tier1.test.ts` — tests for error log append/read, merge success-clears-errors, merge failure-increments-attemptCount, merge routes errors to log
+- `cli/lib/catalog.ts` — `ErrorRecord` type, error log functions, update `Tier1Result`, update `mergeTier1Results` signature and implementation
+- `cli/commands/skill.ts` — update `processBatch` to pass `errorLogPath` to merge, update `catalog errors` subcommand, add `--prune` flag
+- `cli/test/catalog-tier1.test.ts` — tests for error log append/read, merge success-clears-errors, merge failure-increments-attemptCount, merge routes errors to log
 - `context/skills/.gitignore` — add `.catalog-errors.ndjson`
 
 ## Tasks

.claude/plans/.archive/agents-tool-improvement/phase/2-mechanical-compute.md

@@ -24,9 +24,9 @@ Implement native TypeScript functions for mechanical analysis (content hash, wor
 
 | Deliverable | Location | Format |
 |-------------|----------|--------|
-| 5 compute functions | `.scripts/lib/catalog.ts` | TypeScript |
-| Updated `DownloadResult` type | `.scripts/lib/catalog.ts` | TypeScript |
-| Compute function tests | `.scripts/test/catalog-tier1.test.ts` | TypeScript |
+| 5 compute functions | `cli/lib/catalog.ts` | TypeScript |
+| Updated `DownloadResult` type | `cli/lib/catalog.ts` | TypeScript |
+| Compute function tests | `cli/test/catalog-tier1.test.ts` | TypeScript |
 
 ## Files
 
@@ -36,8 +36,8 @@ Implement native TypeScript functions for mechanical analysis (content hash, wor
 
 **Modify:**
 
-- `.scripts/lib/catalog.ts` — add 5 exported compute functions, expand `DownloadResult` type
-- `.scripts/test/catalog-tier1.test.ts` — tests for each compute function including edge cases (empty content, nonexistent dir, headings at various depths)
+- `cli/lib/catalog.ts` — add 5 exported compute functions, expand `DownloadResult` type
+- `cli/test/catalog-tier1.test.ts` — tests for each compute function including edge cases (empty content, nonexistent dir, headings at various depths)
 
 ## Tasks
 

.claude/plans/.archive/agents-tool-improvement/phase/3-incremental-skip-retry.md

@@ -25,20 +25,20 @@ Make `analyze` skip already-analyzed skills by default and add `--retry-errors`
 
 | Deliverable | Location | Format |
 |-------------|----------|--------|
-| `filterForProcessing` function | `.scripts/lib/catalog.ts` | TypeScript |
-| Updated CLI args | `.scripts/commands/skill.ts` | TypeScript |
-| Progress output | `.scripts/commands/skill.ts` | TypeScript |
-| Filter tests | `.scripts/test/catalog-tier1.test.ts` | TypeScript |
+| `filterForProcessing` function | `cli/lib/catalog.ts` | TypeScript |
+| Updated CLI args | `cli/commands/skill.ts` | TypeScript |
+| Progress output | `cli/commands/skill.ts` | TypeScript |
+| Filter tests | `cli/test/catalog-tier1.test.ts` | TypeScript |
 
 ## Files
 
 **Create:**
 - None
 
 **Modify:**
-- `.scripts/lib/catalog.ts` — add `filterForProcessing` function
-- `.scripts/commands/skill.ts` — replace `filterAvailable` call with `filterForProcessing`, add `--retry-errors` flag, update progress output, update `--force` flag semantics
-- `.scripts/test/catalog-tier1.test.ts` — tests for all flag combinations and edge cases
+- `cli/lib/catalog.ts` — add `filterForProcessing` function
+- `cli/commands/skill.ts` — replace `filterAvailable` call with `filterForProcessing`, add `--retry-errors` flag, update progress output, update `--force` flag semantics
+- `cli/test/catalog-tier1.test.ts` — tests for all flag combinations and edge cases
 
 ## Tasks
 

.claude/plans/.archive/agents-tool-improvement/phase/4-agent-prompt-integration.md

@@ -25,11 +25,11 @@ Wire the mechanical compute functions (Phase 2) into `preDownloadSkills`, reduce
 
 | Deliverable | Location | Format |
 |-------------|----------|--------|
-| Updated `preDownloadSkills` | `.scripts/commands/skill.ts` | TypeScript |
-| Reduced agent prompt | `.scripts/commands/skill.ts` | TypeScript |
-| Updated merge logic in `processBatch` | `.scripts/commands/skill.ts` | TypeScript |
-| `validateBatchResults` function | `.scripts/lib/catalog.ts` | TypeScript |
-| Validation tests | `.scripts/test/catalog-tier1.test.ts` | TypeScript |
+| Updated `preDownloadSkills` | `cli/commands/skill.ts` | TypeScript |
+| Reduced agent prompt | `cli/commands/skill.ts` | TypeScript |
+| Updated merge logic in `processBatch` | `cli/commands/skill.ts` | TypeScript |
+| `validateBatchResults` function | `cli/lib/catalog.ts` | TypeScript |
+| Validation tests | `cli/test/catalog-tier1.test.ts` | TypeScript |
 | Integration test results | Manual test batch | NDJSON |
 
 ## Files
@@ -40,9 +40,9 @@ Wire the mechanical compute functions (Phase 2) into `preDownloadSkills`, reduce
 
 **Modify:**
 
-- `.scripts/lib/catalog.ts` — add `validateBatchResults` function
-- `.scripts/commands/skill.ts` — update `preDownloadSkills` to call compute functions, update manifest format, rewrite agent prompt, change `ALLOWED_TOOLS`, update `processBatch` merge logic and error routing, call `validateBatchResults` after merge
-- `.scripts/test/catalog-tier1.test.ts` — tests for validation function
+- `cli/lib/catalog.ts` — add `validateBatchResults` function
+- `cli/commands/skill.ts` — update `preDownloadSkills` to call compute functions, update manifest format, rewrite agent prompt, change `ALLOWED_TOOLS`, update `processBatch` merge logic and error routing, call `validateBatchResults` after merge
+- `cli/test/catalog-tier1.test.ts` — tests for validation function
 
 ## Tasks
 

.claude/plans/.archive/agents-tool-improvement/phase/5-migration-validation.md

@@ -29,10 +29,10 @@ Implement the `catalog scrub` backfill command, run it to clean existing data, v
 
 | Deliverable | Location | Format |
 |-------------|----------|--------|
-| `catalog scrub` subcommand | `.scripts/commands/skill.ts` | TypeScript |
-| Updated `catalog cleanup` | `.scripts/commands/skill.ts` | TypeScript |
-| Updated `catalog forks` | `.scripts/commands/skill.ts` | TypeScript |
-| Updated `catalog summary` | `.scripts/commands/skill.ts` | TypeScript |
+| `catalog scrub` subcommand | `cli/commands/skill.ts` | TypeScript |
+| Updated `catalog cleanup` | `cli/commands/skill.ts` | TypeScript |
+| Updated `catalog forks` | `cli/commands/skill.ts` | TypeScript |
+| Updated `catalog summary` | `cli/commands/skill.ts` | TypeScript |
 | Backfilled catalog | `context/skills/.catalog.ndjson` | NDJSON (gitignored) |
 | Backfilled error log | `context/skills/.catalog-errors.ndjson` | NDJSON (gitignored) |
 | Validation test batch output | Manual | Console output |
@@ -45,8 +45,8 @@ Implement the `catalog scrub` backfill command, run it to clean existing data, v
 
 **Modify:**
 
-- `.scripts/commands/skill.ts` — add `catalog scrub` subcommand, update `catalog cleanup`, `catalog forks`, and `catalog summary` for new data model
-- `.scripts/test/catalog-tier1.test.ts` — tests for scrub logic
+- `cli/commands/skill.ts` — add `catalog scrub` subcommand, update `catalog cleanup`, `catalog forks`, and `catalog summary` for new data model
+- `cli/test/catalog-tier1.test.ts` — tests for scrub logic
 
 ## Tasks
 
@@ -114,7 +114,7 @@ Implement the `catalog scrub` backfill command, run it to clean existing data, v
 - [ ] Verify: `catalog summary` shows accurate counts with attemptCount distribution
 - [ ] Run test batch: `just agents skill catalog analyze --force --limit 1 --batch-size 5`
 - [ ] Verify test batch: real content hashes, no stale errors, attemptCount reset on success, `validateBatchResults` reports 0 issues
-- [ ] Run all tests: `cd .scripts && bun test`
+- [ ] Run all tests: `cd cli && bun test`
 
 ## Notes