fix(ci): root-cause three workflow failures blocking Dependabot PRs (#6)

* fix(ci): three workflow root-causes blocking Dependabot PRs

1. ci.yml — Pkg.instantiate() failed with `expected package
   Cliodynamics [...] to be registered`. The project depends on
   hyperpolymath-internal packages (Cliodynamics, Causals, ZeroProb)
   that live in hyperpolymath/julia-ecosystem's General registry, not
   the public Julia General. Add a step that clones the meta-repo and
   copies registries/General into ~/.julia/registries/HyperpolymathGeneral
   before instantiate. (Pkg can't add a registry from a subdir directly,
   so we install it manually.) Also force-add upstream General as a
   fallback for cold caches.

2. codeql.yml — language matrix was `javascript-typescript` on a
   Julia-only repo; CodeQL exited with a configuration error every
   run. Switch to `actions` (matches the fix already shipped to
   JuliaKids.jl#7 and PRComms.jl#7 in this org).

3. hypatia-scan.yml — used `working-directory: ${{ env.HOME }}/hypatia`
   which evaluated to `/hypatia` (env.HOME is not a GHA context — only
   shell $HOME is). Replaced with the current canonical workflow from
   hyperpolymath/hypatia which uses `cd "$HOME/hypatia"` inside the run
   script and builds a fresh escript when needed.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(ci): use Pkg.Registry.add(path=…) to install hyperpolymath subdir registry

Julia 1.11 ignores raw directory drops into ~/.julia/registries (it uses
the compressed-registry format with <name>.toml + tarball). Switch to
the documented Pkg.Registry.add(RegistrySpec(path=…)) approach. Init the
subdir as its own git repo so Pkg treats it as a bare-clone source.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(ci): install hyperpolymath-internal Julia deps from git URLs

The 'General' registry at hyperpolymath/julia-ecosystem/registries/General
is just a mirror of upstream JuliaRegistries/General — it has the same
name+UUID+repo URL and does NOT contain Cliodynamics, Causals, or
ZeroProb. So pointing Pkg at it changes nothing; the path-based add we
had collapsed into the existing General registry on dedup.

Switch to direct Pkg.add(url=…) for each internal dep. The packages
each have a Project.toml with the matching name+UUID, so Pkg resolves
them cleanly without registry support.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(ci): batch internal-dep Pkg.add into single call

Adding Cliodynamics/Causals/ZeroProb one-at-a-time failed: each Pkg.add
re-resolves the whole project, and on call #1 the other two unregistered
deps still cause check_registered to error out before the URL we just
supplied is considered. Bundling all three PackageSpecs into one
Pkg.add gives the resolver every git source up-front.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(ci): also Pkg.add AcceleratorGate.jl (transitive via Causals + ZeroProb)

Causals and ZeroProb both list AcceleratorGate in their [deps].
AcceleratorGate isn't registered either, so without its URL the
resolver aborts with 'Unsatisfiable requirements detected'.

Note: this still depends on hyperpolymath/Causals.jl#4 landing first
(removes 9 fictional hardware-accelerator weakdeps with placeholder
UUIDs that no resolver can find).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(deps): declare StringDistances dependency

src/parsers.jl line 12 does `using StringDistances` but the package was
missing from Project.toml [deps]. Julia 1.11 precompile failed with:

    ArgumentError: Package InvestigativeJournalist does not have
    StringDistances in its dependencies

StringDistances is a registered package (uuid 88034a9c-...). Add it to
[deps] and constrain to compat = "0.11" (current major).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: hyperpolymath

.github/workflows/ci.yml

@@ -35,5 +35,27 @@ jobs:
 
       - uses: julia-actions/cache@e33b4bfa0ea7cd9caedd7cb82b0e36956ef40285 # v2
 
+      - name: Install hyperpolymath-internal Julia deps from git
+        # These hyperpolymath org-internal packages are NOT in any Julia
+        # registry — the `registries/General` subdir of
+        # hyperpolymath/julia-ecosystem is just a mirror of upstream
+        # JuliaRegistries/General and doesn't contain them.
+        #
+        # The list is the transitive closure of internal deps from this
+        # project's Project.toml: Cliodynamics, Causals, ZeroProb are
+        # direct; AcceleratorGate is needed because Causals + ZeroProb
+        # depend on it. Install all in a SINGLE Pkg.add call so the
+        # resolver knows about all the git sources at once.
+        run: |
+          julia --project=. -e '
+            using Pkg
+            Pkg.add([
+              Pkg.PackageSpec(url="https://github.com/hyperpolymath/Cliodynamics.jl"),
+              Pkg.PackageSpec(url="https://github.com/hyperpolymath/Causals.jl"),
+              Pkg.PackageSpec(url="https://github.com/hyperpolymath/ZeroProb.jl"),
+              Pkg.PackageSpec(url="https://github.com/hyperpolymath/AcceleratorGate.jl"),
+            ])
+          '
+
       - name: Install, build, test
         run: julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.build(); Pkg.test()'

.github/workflows/codeql.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - language: javascript-typescript
+          - language: actions
             build-mode: none
 
     steps:

Project.toml

@@ -19,6 +19,7 @@ MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Gumbo = "708ec375-b3d6-5a57-a7ce-8257bf98657a"
 Cascadia = "54eefc05-d75b-58de-a785-1a3403f0919f"
 DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+StringDistances = "88034a9c-02f8-509d-84a9-84ec65e18404"
 Cliodynamics = "8d2f3e70-4c6b-5e9c-a3d1-2f8e9c0b1d2e"
 Causals = "c4a8b6d2-f9e3-4c1a-b8d7-9f2e3c4d5e6f"
 ZeroProb = "f9e8c2e0-8b4a-4d5f-9a3c-1e2d3c4b5a6f"
@@ -40,6 +41,7 @@ MetaGraphsNext = "0.7"
 Gumbo = "0.8"
 Cascadia = "1"
 DuckDB = "1"
+StringDistances = "0.11"
 Cliodynamics = "1"
 Causals = "0.2"
 ZeroProb = "0.1"