create-academic-research 0.1.13 → 0.1.15

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. package/README.md +71 -11
  2. package/dist/bin/academic-research.js +0 -0
  3. package/dist/bin/create-academic-research.js +0 -0
  4. package/dist/src/capabilities.d.ts +132 -3
  5. package/dist/src/capabilities.js +993 -48
  6. package/dist/src/cli.js +448 -33
  7. package/dist/src/mcp-env.d.ts +4 -0
  8. package/dist/src/mcp-env.js +2 -2
  9. package/dist/src/mcp-probe.d.ts +3 -2
  10. package/dist/src/mcp-probe.js +87 -30
  11. package/dist/src/project.d.ts +18 -0
  12. package/dist/src/project.js +654 -22
  13. package/dist/src/stack.d.ts +38 -0
  14. package/dist/src/stack.js +260 -14
  15. package/package.json +2 -2
  16. package/template/README.md +37 -4
  17. package/template/_gitignore +1 -0
  18. package/template/docs/agent/mcp-client-setup.md +43 -3
  19. package/template/docs/agent/mcp-setup.md +60 -0
  20. package/template/docs/getting-started.md +17 -5
  21. package/template/package.json +7 -1
package/template/docs/getting-started.md CHANGED
@@ -7,12 +7,23 @@ Use this path for the first working session in a new research repository.
7
7
  ```bash
8
8
  npm install
9
9
  npm run doctor
10
+ npm run update
10
11
  npm run setup
11
12
  ```
12
13
 
13
- `doctor` checks required files and structural contracts. `setup` prints the
14
- active skill preset, installed skill count, enabled MCP records, and next
15
- commands without changing files.
14
+ `doctor` checks required files and structural contracts. `update` uses
15
+ `create-academic-research@latest` and is a dry-run unless you pass
16
+ `-- --apply`. Safe scaffold files are tracked in
17
+ `.academic-research/managed-files.json`; locally edited files are skipped
18
+ instead of overwritten. `setup` prints the active skill preset, installed skill
19
+ count, enabled MCP records, and next commands without changing files.
20
+
21
+ If an older project still has a pinned `update` script, run:
22
+
23
+ ```bash
24
+ npm exec --yes --package=create-academic-research@latest -- academic-research update --root .
25
+ npm exec --yes --package=create-academic-research@latest -- academic-research update --root . --apply
26
+ ```
16
27
 
17
28
  ## 2. Install Project-Local Skills
18
29
 
@@ -42,8 +53,9 @@ npm run mcp:env -- openalex semantic-scholar zotero
42
53
  npm run mcp:doctor -- --env-file .env.local
43
54
  ```
44
55
 
45
- `mcp smoke` is a non-launching readiness check. `mcp probe` is opt-in and starts
46
- MCP processes for a real stdio handshake.
56
+ `mcp smoke` is a non-launching readiness check. `mcp probe` is opt-in: local
57
+ stdio servers get a real handshake, while remote endpoints are reported as
58
+ configured without a network probe.
47
59
 
48
60
  ```bash
49
61
  npm run mcp:smoke -- --env-file .env.local
package/template/package.json CHANGED
@@ -4,6 +4,7 @@
4
4
  "type": "module",
5
5
  "scripts": {
6
6
  "doctor": "npm exec --yes --package=create-academic-research@latest -- academic-research doctor",
7
+ "update": "npm exec --yes --package=create-academic-research@latest -- academic-research update",
7
8
  "setup": "npm exec --yes --package=create-academic-research@latest -- academic-research setup",
8
9
  "rename": "npm exec --yes --package=create-academic-research@latest -- academic-research rename",
9
10
  "agents:list": "npm exec --yes --package=create-academic-research@latest -- academic-research agents list",
@@ -15,6 +16,8 @@
15
16
  "skills:uninstall": "npm exec --yes --package=create-academic-research@latest -- academic-research skills uninstall",
16
17
  "skills:update": "npm exec --yes --package=create-academic-research@latest -- academic-research skills update",
17
18
  "mcp:list": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp list",
19
+ "mcp:modes": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp modes",
20
+ "mcp:status": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp status",
18
21
  "mcp:enabled": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp enabled",
19
22
  "mcp:available": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp available",
20
23
  "mcp:commands": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp commands",
@@ -22,6 +25,9 @@
22
25
  "mcp:dotenv": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp env --write .env.example --all",
23
26
  "mcp:enable": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp enable",
24
27
  "mcp:disable": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp disable",
28
+ "mcp:setup": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp setup",
29
+ "mcp:client:add": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp client add",
30
+ "mcp:client:remove": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp client remove",
25
31
  "mcp:install": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp install",
26
32
  "mcp:uninstall": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp uninstall",
27
33
  "mcp:smoke": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp smoke",
@@ -29,6 +35,6 @@
29
35
  "mcp:probe": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp probe"
30
36
  },
31
37
  "devDependencies": {
32
- "create-academic-research": "0.1.13"
38
+ "create-academic-research": "0.1.14"
33
39
  }
34
40
  }