feat: update Dockerfiles and configuration for TLS support across multiple modules

Signed-off-by: d9pouces <github@19pouces.net>

id_configurator/modules/certificates.py

@@ -1,15 +1,52 @@
+# noinspection SpellCheckingInspection
 """Install root certificates into the system's CA store.
 
 Certificates from the configuration are dropped into the "local" CA
-directory, then the real `update-ca-certificates` binary is invoked to
-rebuild the trust store (bundle + hashed symlinks) exactly like it would on
-a real Debian/Ubuntu system, instead of reimplementing that logic here.
+directory, then the trust store under `/etc/ssl/certs` (bundle + named
+symlinks) is rebuilt in pure Python, mirroring what Debian's
+`update-ca-certificates` shell script does: every certificate enabled in
+`ca-certificates.conf` (read from `<src>`), plus everything found under the
+local certificates directory, is concatenated into a single bundle file and
+gets a `<name>.pem` symlink pointing at it.
+
+The OpenSSL subject-hash symlinks (`<hash>.0`) that `update-ca-certificates`
+also creates, for CApath-style directory lookups, are intentionally not
+reproduced here: none of this tool's own consumers (pip, apt, dnf, apk, the
+JVM, ...) do CApath lookups, they all read the single bundle file.
+
+If `/etc/ssl/certs` is itself a symlink in `<src>` (as on RHEL, where it
+points to `/etc/pki/tls/certs`), the bundle and symlinks are written to
+whatever directory it resolves to instead. The write lands where the
+deployed system will actually look, without ever writing a plain directory
+where that system expects a symlink. In that case `/usr/lib/ssl/cert.pem`
+(see below) is not written either, since it isn't OpenSSL's default CAfile
+on such systems in the first place.
+
+Otherwise, `/usr/lib/ssl/cert.pem` - OpenSSL's own compiled-in default
+CAfile on Debian/Ubuntu, and what apt's own https method reads absent any
+explicit configuration - is symlinked to the rebuilt bundle too. This is
+normally created by the ca-certificates package's postinst script; doing it
+here as well means the bundle is trusted even on a base image that never
+had that package installed.
+
+When `<src>` also has a RHEL/Fedora-style trust store (`/etc/pki/ca-trust`),
+the configured certificates are additionally dropped into
+`/etc/pki/ca-trust/source/anchors` and merged into
+`/etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem`, the single file that
+`/etc/pki/tls/certs/ca-bundle.crt` and OpenSSL's own default CAfile
+(`/etc/pki/tls/cert.pem`) both resolve to on such systems - which is what
+dnf/curl/openssl-based tools there actually read. This intentionally does
+not reproduce the rest of `update-ca-trust extract`'s output (the OpenSSL
+"trust" bundle with per-certificate usage flags, the email/objsign bundles,
+the extracted Java keystore, ...); only the plain PEM trust bundle is
+rebuilt.
 """
 
 from __future__ import annotations
 
 import logging
-import subprocess
+import posixpath
+from pathlib import Path
 
 from id_configurator.context import Context
 from id_configurator.modules.base import Module, register
@@ -17,11 +54,85 @@ from id_configurator.modules.base import Module, register
 logger = logging.getLogger(__name__)
 
 _LOCAL_CERTS_DIR = "usr/local/share/ca-certificates"
+# noinspection SpellCheckingInspection
 _CERTSCONF = "etc/ca-certificates.conf"
+# noinspection SpellCheckingInspection
 _CERTSDIR = "usr/share/ca-certificates"
+# noinspection SpellCheckingInspection
 _ETCCERTSDIR = "etc/ssl/certs"
+_CERT_BUNDLE = "ca-certificates.crt"
+
+_RHEL_ANCHORS_DIR = "etc/pki/ca-trust/source/anchors"
+_RHEL_EXTRACTED_BUNDLE = "etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem"
+
+# OpenSSL's own compiled-in default CAfile on Debian/Ubuntu (OPENSSLDIR is
+# /usr/lib/ssl there); the ca-certificates package's postinst symlinks this
+# to the bundle, which is what lets OpenSSL-linked tools (including apt's
+# own https method) find it without any explicit CAfile configuration. That
+# symlink only exists once the package has actually been installed, so it is
+# created here too, making the bundle usable even on a base image that
+# never had ca-certificates installed at all.
+_OPENSSL_DEFAULT_CERT_FILE = "usr/lib/ssl/cert.pem"
 
 
+def _pem_name(relative_crt: str) -> str:
+    # noinspection GrazieInspection
+    """Mirror update-ca-certificates' `.pem` symlink naming for a `*.crt` path."""
+    stem = Path(relative_crt).name.removesuffix(".crt")
+    stem = stem.replace(" ", "_").replace("(", "=").replace(")", "=").replace(",", "_")
+    return f"{stem}.pem"
+
+
+def _ensure_trailing_newline(content: bytes) -> bytes:
+    return content if content.endswith(b"\n") else content + b"\n"
+
+
+def _resolve_target_dir(context: Context, relative: str) -> str:
+    """Resolve `relative` against `<src>`, following it if it is a symlink.
+
+    Some systems replace a well-known directory with a symlink to another
+    location (e.g. RHEL's `/etc/ssl/certs` -> `/etc/pki/tls/certs`). Writing
+    to the literal path in that case would create a plain directory where
+    the deployed system expects a symlink - which BuildKit refuses to
+    overlay a directory onto in the first place - while leaving the actual,
+    symlinked-to location untouched. Returns `relative` unchanged if it
+    isn't a symlink in `<src>`, or if it can't be resolved back to a path
+    under `<src>`.
+    """
+    if context.src is None:
+        return relative
+    # Not context.src_path(): it resolves symlinks away before we can even
+    # check for one.
+    source = context.src / relative
+    if not source.is_symlink():
+        return relative
+    target = source.readlink()
+    if target.is_absolute():
+        return posixpath.normpath(target.as_posix()).lstrip("/")
+    resolved = (source.parent / target).resolve()
+    try:
+        return resolved.relative_to(context.src.resolve()).as_posix()
+    except ValueError:
+        return relative
+
+
+# noinspection SpellCheckingInspection
+def _parse_certsconf(certsconf: Path) -> list[str]:
+    """Return the paths (relative to CERTSDIR) enabled in ca-certificates.conf.
+
+    Blank lines and comments (`#`) are ignored; lines prefixed with `!`
+    are explicitly disabled, exactly like update-ca-certificates.
+    """
+    enabled = []
+    for line in certsconf.read_text(encoding="utf-8").splitlines():
+        line = line.strip()
+        if not line or line.startswith("#") or line.startswith("!"):
+            continue
+        enabled.append(line)
+    return enabled
+
+
+# noinspection SpellCheckingInspection
 @register
 class CertificatesModule(Module):
     name = "certificates"
@@ -46,37 +157,90 @@ class CertificatesModule(Module):
             )
             logger.info("installed root certificate %s", certificate.name)
         self._update_ca_certificates_conf(context)
+        if self._rhel_trust_store_present(context):
+            self._update_rhel_trust_store(context, configured_names)
 
     @staticmethod
-    def _update_ca_certificates_conf(context: Context) -> None:
-        etccertsdir = context.dst_path(_ETCCERTSDIR)
+    def _rhel_trust_store_present(context: Context) -> bool:
+        anchors = context.src_path(_RHEL_ANCHORS_DIR)
+        return anchors is not None and anchors.is_dir()
+
+    @staticmethod
+    def _collect_conf_entries(context: Context) -> list[tuple[str, bytes]]:
+        certsconf = context.src_path(_CERTSCONF)
+        certsdir = context.src_path(_CERTSDIR)
+        if certsconf is None or not certsconf.is_file() or certsdir is None:
+            return []
+        entries = []
+        for relative in _parse_certsconf(certsconf):
+            source = certsdir / relative
+            if not source.is_file():
+                logger.warning("%s not found, but listed in %s", source, certsconf)
+                continue
+            entries.append((f"{_CERTSDIR}/{relative}", source.read_bytes()))
+        return entries
+
+    @staticmethod
+    def _collect_local_entries(localcertsdir: Path) -> list[tuple[str, bytes]]:
+        entries = []
+        for source in sorted(localcertsdir.rglob("*.crt")):
+            relative = source.relative_to(localcertsdir).as_posix()
+            entries.append((f"{_LOCAL_CERTS_DIR}/{relative}", source.read_bytes()))
+        return entries
+
+    @classmethod
+    def _update_ca_certificates_conf(cls, context: Context) -> None:
+        etccertsdir_relative = _resolve_target_dir(context, _ETCCERTSDIR)
+        etccertsdir = context.dst_path(etccertsdir_relative)
         localcertsdir = context.dst_path(_LOCAL_CERTS_DIR)
         etccertsdir.mkdir(parents=True, exist_ok=True)
         localcertsdir.mkdir(parents=True, exist_ok=True)
 
-        args = [
-            "update-ca-certificates",
-            "--etccertsdir",
-            str(etccertsdir),
-            "--localcertsdir",
-            str(localcertsdir),
-        ]
-        certsconf = context.src_path(_CERTSCONF)
-        if certsconf is not None and certsconf.is_file():
-            args += ["--certsconf", str(certsconf)]
-        certsdir = context.src_path(_CERTSDIR)
-        if certsdir is not None and certsdir.is_dir():
-            args += ["--certsdir", str(certsdir)]
+        # Same processing order as update-ca-certificates: ca-certificates.conf
+        # entries first, then everything under the local certificate directory.
+        entries = cls._collect_conf_entries(context) + cls._collect_local_entries(
+            localcertsdir
+        )
 
-        logger.debug("running: %s", " ".join(args))
-        try:
-            result = subprocess.run(args, check=True, capture_output=True, text=True)
-        except FileNotFoundError as exc:
-            raise RuntimeError(
-                "update-ca-certificates is not available; the ca-certificates package must be installed "
-                "in the environment running id-configurator"
-            ) from exc
-        except subprocess.CalledProcessError as exc:
-            raise RuntimeError(f"update-ca-certificates failed:\n{exc.stderr}") from exc
-        if result.stderr:
-            logger.debug("%s", result.stderr.strip())
+        bundle = bytearray()
+        for relative, content in entries:
+            bundle += _ensure_trailing_newline(content)
+            pem_path = etccertsdir / _pem_name(relative)
+            pem_path.unlink(missing_ok=True)
+            pem_path.symlink_to(f"/{relative}")
+
+        context.write_file(f"{etccertsdir_relative}/{_CERT_BUNDLE}", bytes(bundle))
+        logger.info("rebuilt %s from %d certificate(s)", _CERT_BUNDLE, len(entries))
+
+        if etccertsdir_relative == _ETCCERTSDIR:
+            cert_file = context.dst_path(_OPENSSL_DEFAULT_CERT_FILE)
+            cert_file.parent.mkdir(parents=True, exist_ok=True)
+            cert_file.unlink(missing_ok=True)
+            cert_file.symlink_to(f"/{etccertsdir_relative}/{_CERT_BUNDLE}")
+
+    @staticmethod
+    def _update_rhel_trust_store(context: Context, configured_names: set[str]) -> None:
+        for existing in context.iter_src_dir(_RHEL_ANCHORS_DIR):
+            if existing.stem not in configured_names:
+                context.write_file(
+                    f"{_RHEL_ANCHORS_DIR}/{existing.name}", existing.read_bytes()
+                )
+        for certificate in context.config.configurations.certificates:
+            context.write_file(
+                f"{_RHEL_ANCHORS_DIR}/{certificate.name}.crt",
+                certificate.content.encode(),
+            )
+
+        bundle = bytearray()
+        existing_bundle = context.read_src_file(_RHEL_EXTRACTED_BUNDLE)
+        if existing_bundle is not None:
+            bundle += _ensure_trailing_newline(existing_bundle)
+
+        # Every write above went through context.write_file(), which only ever
+        # creates regular files, so every entry here is a certificate to add.
+        anchors = sorted(context.dst_path(_RHEL_ANCHORS_DIR).iterdir())
+        for anchor in anchors:
+            bundle += _ensure_trailing_newline(anchor.read_bytes())
+
+        context.write_file(_RHEL_EXTRACTED_BUNDLE, bytes(bundle))
+        logger.info("rebuilt RHEL/Fedora trust store from %d anchor(s)", len(anchors))

id_configurator/modules/java.py

@@ -43,8 +43,8 @@ from pathlib import Path
 import jks
 from cryptography import x509
 from cryptography.hazmat.primitives.serialization import (
-    BestAvailableEncryption,
     Encoding,
+    NoEncryption,
     pkcs12,
 )
 
@@ -87,9 +87,13 @@ def _add_to_pkcs12(
     entries = list(loaded.additional_certs)
     for named, cert in zip(certificates, certs, strict=True):
         entries.append(pkcs12.PKCS12Certificate(cert, named.name.encode("utf-8")))
-    return pkcs12.serialize_java_truststore(
-        entries, BestAvailableEncryption(_STORE_PASSWORD)
-    )
+    # Trust-only entries must stay unencrypted, matching how the JDK's own
+    # cacerts is built: JVM code that never sets javax.net.ssl.trustStore*
+    # (e.g. Maven) loads the default truststore with a null password, which
+    # can only skip the integrity check, not decrypt encrypted entries.
+    # Encrypting them here (e.g. with BestAvailableEncryption) silently
+    # yields zero usable trust anchors for every such caller.
+    return pkcs12.serialize_java_truststore(entries, NoEncryption())
 
 
 def _add_to_jks(

tests/configs/Apk.yaml.j2

@@ -2,13 +2,16 @@ uuid: 3d2f6a44-8b19-4c2b-9e7a-1f5c8a2d6b90
 organisation: InterDiode
 description: Apk test configuration
 configurations:
-  certificates: []
+  certificates:
+  - name: Test CA
+    content: |
+{{ 'certs/test-ca.crt.pem' | file | indent(6, first=true) }}
   apt:
     sources: []
     keys: []
   apk:
     repositories:
-    - url: http://host.docker.internal:{{ 'APK_REPO_PORT' | env }}/
+    - url: https://host.docker.internal:{{ 'APK_REPO_PORT' | env }}/
       key: |
 {{ 'dockerfiles/repos/040d0af5f97a0a44.rsa.pub' | file | indent(8, first=true) }}
   yum:

tests/configs/Java.yaml.j2

@@ -2,7 +2,10 @@ uuid: 6a1d4e2c-9f3b-4a5d-8c7e-2b1f9a6d4c3e
 organisation: InterDiode
 description: Java test configuration
 configurations:
-  certificates: []
+  certificates:
+  - name: Test CA
+    content: |
+{{ 'certs/test-ca.crt.pem' | file | indent(6, first=true) }}
   apt:
     sources: []
     keys: []
@@ -16,4 +19,4 @@ configurations:
   java:
     repositories:
     - name: central
-      url: http://host.docker.internal:{{ 'JAVA_REPO_PORT' | env }}/
+      url: https://host.docker.internal:{{ 'JAVA_REPO_PORT' | env }}/

tests/configs/Yum.yaml.j2

@@ -2,7 +2,10 @@ uuid: 8f6a0e2a-5b7a-4d2c-9d1a-3c2b6b9c4b7e
 organisation: InterDiode
 description: Yum test configuration
 configurations:
-  certificates: []
+  certificates:
+  - name: Test CA
+    content: |
+{{ 'certs/test-ca.crt.pem' | file | indent(6, first=true) }}
   apt:
     sources: []
     keys: []
@@ -11,7 +14,7 @@ configurations:
   yum:
     repositories:
     - name: demo
-      index-url: http://host.docker.internal:{{ 'YUM_REPO_PORT' | env }}/
+      index-url: https://host.docker.internal:{{ 'YUM_REPO_PORT' | env }}/
     keys: []
   python:
     repositories: []

tests/dockerfiles/Apk.Dockerfile

@@ -1,5 +1,5 @@
 FROM alpine:3.20 AS detection
-FROM interdiode/id_configurator:latest AS configuration
+FROM interdiode/id-configurator:latest AS configuration
 COPY --from=detection / /src/
 COPY --from=generated-config Apk.yaml /config.yaml
 RUN id-configurator apply --config /config.yaml --src /src --dst /dst

tests/dockerfiles/Apt.Dockerfile

@@ -1,10 +1,9 @@
 FROM debian:trixie-slim AS detection
-FROM interdiode/id_configurator:latest AS configuration
+FROM interdiode/id-configurator:latest AS configuration
 COPY --from=detection / /src/
 COPY --from=generated-config Apt.yaml /config.yaml
 RUN id-configurator apply --config /config.yaml --src /src --dst /dst
 FROM debian:trixie-slim AS runtime
-RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates
 COPY --from=configuration /dst/ /
 RUN apt-get update \
     && apt-get install -y --no-install-recommends idconfiguratortestpkg \

tests/dockerfiles/Java.Dockerfile

@@ -1,5 +1,5 @@
 FROM maven:3.9-eclipse-temurin-21 AS detection
-FROM interdiode/id_configurator:latest AS configuration
+FROM interdiode/id-configurator:latest AS configuration
 COPY --from=detection / /src/
 COPY --from=generated-config Java.yaml /config.yaml
 RUN id-configurator apply --config /config.yaml --src /src --dst /dst

tests/dockerfiles/Python.Dockerfile

@@ -1,5 +1,5 @@
 FROM python:3.13-slim AS detection
-FROM interdiode/id_configurator:latest AS configuration
+FROM interdiode/id-configurator:latest AS configuration
 COPY --from=detection / /src/
 COPY --from=generated-config Python.yaml /config.yaml
 RUN id-configurator apply --config /config.yaml --src /src --dst /dst

tests/dockerfiles/Yum.Dockerfile

@@ -1,5 +1,5 @@
 FROM rockylinux:9 AS detection
-FROM interdiode/id_configurator:latest AS configuration
+FROM interdiode/id-configurator:latest AS configuration
 COPY --from=detection / /src/
 COPY --from=generated-config Yum.yaml /config.yaml
 RUN id-configurator apply --config /config.yaml --src /src --dst /dst

tests/dockerfiles/repos/apk-repo.Dockerfile

@@ -1,6 +1,7 @@
 # Minimal Alpine (apk) repository with a signed index, serving one hand-built
-# .apk package over plain HTTP, used by tox-docker to exercise the `apk`
-# module integration test (tests/configs/Apk.yaml.tmpl,
+# .apk package over TLS, using the same Test CA as the pypi-repo/apt-repo/
+# yum-repo fixtures, used by tox-docker to exercise the `apk` module
+# integration test (tests/configs/Apk.yaml.j2,
 # tests/dockerfiles/Apk.Dockerfile). The package is signed with the static
 # key pair 040d0af5f97a0a44.rsa / 040d0af5f97a0a44.rsa.pub, whose public
 # half is what the `apk` module configuration is expected to install into
@@ -39,5 +40,7 @@ RUN arch_dir=$(ls /home/builder/packages/builder) \
 
 FROM nginx:alpine
 COPY --from=packagebuild /srv /srv
+COPY repo-server.crt.pem /etc/nginx/certs/repo-server.crt.pem
+COPY repo-server.key.pem /etc/nginx/certs/repo-server.key.pem
 COPY apk-repo.nginx.conf /etc/nginx/conf.d/default.conf
 EXPOSE 8443

tests/dockerfiles/repos/apk-repo.nginx.conf

@@ -1,7 +1,10 @@
 server {
-    listen 8443 default_server;
+    listen 8443 ssl default_server;
     server_name _;
 
+    ssl_certificate     /etc/nginx/certs/repo-server.crt.pem;
+    ssl_certificate_key /etc/nginx/certs/repo-server.key.pem;
+
     root /srv;
     autoindex off;
 }

tests/dockerfiles/repos/java-repo.Dockerfile

@@ -1,6 +1,7 @@
-# Minimal Maven-compatible repository serving one hand-built jar over plain
-# HTTP, used by tox-docker to exercise the `java` module integration test
-# (tests/configs/Java.yaml.tmpl, tests/dockerfiles/Java.Dockerfile).
+# Minimal Maven-compatible repository serving one hand-built jar over TLS,
+# using the same Test CA as the pypi-repo/apt-repo/yum-repo/apk-repo
+# fixtures, used by tox-docker to exercise the `java` module integration
+# test (tests/configs/Java.yaml.j2, tests/dockerfiles/Java.Dockerfile).
 #
 # Built by tox-docker, whose build context is this directory (not the repo
 # root) - every COPY source below must live under tests/dockerfiles/repos/.
@@ -10,5 +11,7 @@ RUN python3 /build_test_jar.py
 
 FROM nginx:alpine
 COPY --from=jarbuild /srv /srv
+COPY repo-server.crt.pem /etc/nginx/certs/repo-server.crt.pem
+COPY repo-server.key.pem /etc/nginx/certs/repo-server.key.pem
 COPY java-repo.nginx.conf /etc/nginx/conf.d/default.conf
 EXPOSE 8443

tests/dockerfiles/repos/java-repo.nginx.conf

@@ -1,7 +1,10 @@
 server {
-    listen 8443 default_server;
+    listen 8443 ssl default_server;
     server_name _;
 
+    ssl_certificate     /etc/nginx/certs/repo-server.crt.pem;
+    ssl_certificate_key /etc/nginx/certs/repo-server.key.pem;
+
     root /srv;
     autoindex off;
 }

tests/dockerfiles/repos/yum-repo.Dockerfile

@@ -1,7 +1,7 @@
-# Minimal YUM/DNF repository serving one hand-built RPM package over plain
-# HTTP (gpgcheck is off in the test config, so no TLS/signing is needed),
-# used by tox-docker to exercise the `yum` module integration test
-# (tests/configs/Yum.yaml.tmpl, tests/dockerfiles/Yum.Dockerfile).
+# Minimal YUM/DNF repository serving one hand-built RPM package over TLS,
+# using the same Test CA as the pypi-repo/apt-repo fixtures, used by
+# tox-docker to exercise the `yum` module integration test
+# (tests/configs/Yum.yaml.j2, tests/dockerfiles/Yum.Dockerfile).
 #
 # Built by tox-docker, whose build context is this directory (not the repo
 # root) - every COPY source below must live under tests/dockerfiles/repos/.
@@ -16,5 +16,7 @@ RUN createrepo_c /srv
 
 FROM nginx:alpine
 COPY --from=packagebuild /srv /srv
+COPY repo-server.crt.pem /etc/nginx/certs/repo-server.crt.pem
+COPY repo-server.key.pem /etc/nginx/certs/repo-server.key.pem
 COPY yum-repo.nginx.conf /etc/nginx/conf.d/default.conf
 EXPOSE 8443

tests/dockerfiles/repos/yum-repo.nginx.conf

@@ -1,7 +1,10 @@
 server {
-    listen 8443 default_server;
+    listen 8443 ssl default_server;
     server_name _;
 
+    ssl_certificate     /etc/nginx/certs/repo-server.crt.pem;
+    ssl_certificate_key /etc/nginx/certs/repo-server.key.pem;
+
     root /srv;
     autoindex off;
 }

tests/test_certificates.py

@@ -1,11 +1,10 @@
-import subprocess
-from unittest.mock import MagicMock
-
-import pytest
-
 from id_configurator.config import Configuration
 from id_configurator.context import Context
-from id_configurator.modules.certificates import CertificatesModule
+from id_configurator.modules.certificates import (
+    CertificatesModule,
+    _pem_name,
+    _resolve_target_dir,
+)
 
 CERT_CONTENT = "fake-cert-bytes"
 
@@ -32,38 +31,30 @@ def test_is_relevant_false_when_no_certificates(tmp_path) -> None:
     assert CertificatesModule().is_relevant(context) is False
 
 
-def _mock_success(monkeypatch, stderr: str = "") -> MagicMock:
-    mock_run = MagicMock(
-        return_value=subprocess.CompletedProcess(
-            args=[], returncode=0, stdout="", stderr=stderr
-        )
-    )
-    monkeypatch.setattr("id_configurator.modules.certificates.subprocess.run", mock_run)
-    return mock_run
-
-
-def test_apply_writes_certificate_and_calls_update_ca_certificates(
-    tmp_path, monkeypatch
-) -> None:
-    mock_run = _mock_success(monkeypatch)
+def test_apply_writes_certificate_and_rebuilds_bundle(tmp_path) -> None:
     dst = tmp_path / "dst"
     context = Context(config=make_config(True), dst=dst, src=None)
 
     CertificatesModule().apply(context)
 
-    written = dst / "usr/local/share/ca-certificates/new-root-ca.crt"
-    assert written.read_bytes() == b"fake-cert-bytes"
-    mock_run.assert_called_once()
-    args = mock_run.call_args.args[0]
-    assert args[0] == "update-ca-certificates"
-    assert "--certsconf" not in args
-    assert "--certsdir" not in args
+    local_cert = dst / "usr/local/share/ca-certificates/new-root-ca.crt"
+    assert local_cert.read_bytes() == b"fake-cert-bytes"
+
+    bundle = dst / "etc/ssl/certs/ca-certificates.crt"
+    assert bundle.read_bytes() == b"fake-cert-bytes\n"
+
+    pem = dst / "etc/ssl/certs/new-root-ca.pem"
+    assert pem.is_symlink()
+    assert (
+        pem.readlink().as_posix() == "/usr/local/share/ca-certificates/new-root-ca.crt"
+    )
+
+    openssl_default = dst / "usr/lib/ssl/cert.pem"
+    assert openssl_default.is_symlink()
+    assert openssl_default.readlink().as_posix() == "/etc/ssl/certs/ca-certificates.crt"
 
 
-def test_apply_preserves_existing_local_certificates_from_src(
-    tmp_path, monkeypatch
-) -> None:
-    mock_run = _mock_success(monkeypatch, stderr="some warning")
+def test_apply_merges_conf_listed_and_local_certificates(tmp_path) -> None:
     src = tmp_path / "src"
     local_certs_dir = src / "usr/local/share/ca-certificates"
     local_certs_dir.mkdir(parents=True)
@@ -71,9 +62,14 @@ def test_apply_preserves_existing_local_certificates_from_src(
     (local_certs_dir / "new-root-ca.crt").write_bytes(
         b"stale-bytes-should-be-overwritten"
     )
-    (src / "etc/ca-certificates.conf").parent.mkdir(parents=True)
-    (src / "etc/ca-certificates.conf").write_text("existing.crt\n", encoding="utf-8")
-    (src / "usr/share/ca-certificates").mkdir(parents=True)
+    system_certs_dir = src / "usr/share/ca-certificates"
+    system_certs_dir.mkdir(parents=True)
+    # No trailing newline, to exercise the newline-normalization on append.
+    (system_certs_dir / "system-ca.crt").write_bytes(b"system-ca-bytes")
+    (src / "etc/ca-certificates.conf").parent.mkdir(parents=True, exist_ok=True)
+    (src / "etc/ca-certificates.conf").write_text(
+        "# a comment\n\n!disabled-ca.crt\nsystem-ca.crt\n", encoding="utf-8"
+    )
 
     dst = tmp_path / "dst"
     context = Context(config=make_config(True), dst=dst, src=src)
@@ -84,35 +80,160 @@ def test_apply_preserves_existing_local_certificates_from_src(
     assert (local_dst / "existing.crt").read_bytes() == b"existing-bytes"
     assert (local_dst / "new-root-ca.crt").read_bytes() == b"fake-cert-bytes"
 
-    args = mock_run.call_args.args[0]
-    assert "--certsconf" in args
-    assert str(src / "etc/ca-certificates.conf") in args
-    assert "--certsdir" in args
-    assert str(src / "usr/share/ca-certificates") in args
+    bundle = dst / "etc/ssl/certs/ca-certificates.crt"
+    # ca-certificates.conf entries first, then local certificates sorted by name.
+    assert bundle.read_bytes() == (
+        b"system-ca-bytes\nexisting-bytes\nfake-cert-bytes\n"
+    )
+
+    etc_certs = dst / "etc/ssl/certs"
+    assert (
+        etc_certs / "system-ca.pem"
+    ).readlink().as_posix() == "/usr/share/ca-certificates/system-ca.crt"
+    assert (
+        etc_certs / "existing.pem"
+    ).readlink().as_posix() == "/usr/local/share/ca-certificates/existing.crt"
+    assert (
+        etc_certs / "new-root-ca.pem"
+    ).readlink().as_posix() == "/usr/local/share/ca-certificates/new-root-ca.crt"
+    # The disabled entry must not produce a symlink or appear in the bundle.
+    assert not (etc_certs / "disabled-ca.pem").exists()
 
 
-def test_update_ca_certificates_raises_when_binary_missing(
-    tmp_path, monkeypatch
+def test_apply_warns_and_skips_missing_conf_entry(tmp_path, caplog) -> None:
+    src = tmp_path / "src"
+    (src / "usr/share/ca-certificates").mkdir(parents=True)
+    (src / "etc/ca-certificates.conf").parent.mkdir(parents=True, exist_ok=True)
+    (src / "etc/ca-certificates.conf").write_text("missing.crt\n", encoding="utf-8")
+
+    dst = tmp_path / "dst"
+    context = Context(config=make_config(True), dst=dst, src=src)
+
+    with caplog.at_level("WARNING"):
+        CertificatesModule().apply(context)
+
+    assert "missing.crt" in caplog.text
+    bundle = dst / "etc/ssl/certs/ca-certificates.crt"
+    assert bundle.read_bytes() == b"fake-cert-bytes\n"
+
+
+def test_pem_name_sanitizes_special_characters() -> None:
+    assert _pem_name("usr/share/ca-certificates/New Root, CA.crt") == "New_Root__CA.pem"
+    assert _pem_name("Vendor (Test).crt") == "Vendor_=Test=.pem"
+
+
+def test_apply_skips_rhel_trust_store_when_absent(tmp_path) -> None:
+    dst = tmp_path / "dst"
+    context = Context(config=make_config(True), dst=dst, src=None)
+
+    CertificatesModule().apply(context)
+
+    assert not (dst / "etc/pki").exists()
+
+
+def test_apply_updates_rhel_trust_store_when_present(tmp_path) -> None:
+    src = tmp_path / "src"
+    anchors_dir = src / "etc/pki/ca-trust/source/anchors"
+    anchors_dir.mkdir(parents=True)
+    (anchors_dir / "existing-anchor.pem").write_bytes(b"existing-anchor-bytes")
+    (anchors_dir / "new-root-ca.crt").write_bytes(b"stale-should-be-overwritten")
+    extracted_bundle = src / "etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem"
+    extracted_bundle.parent.mkdir(parents=True)
+    # No trailing newline, to exercise the newline-normalization on append.
+    extracted_bundle.write_bytes(b"vendor-bundle-bytes")
+
+    dst = tmp_path / "dst"
+    context = Context(config=make_config(True), dst=dst, src=src)
+
+    CertificatesModule().apply(context)
+
+    anchors_dst = dst / "etc/pki/ca-trust/source/anchors"
+    assert (
+        anchors_dst / "existing-anchor.pem"
+    ).read_bytes() == b"existing-anchor-bytes"
+    assert (anchors_dst / "new-root-ca.crt").read_bytes() == b"fake-cert-bytes"
+
+    bundle_dst = dst / "etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem"
+    assert bundle_dst.read_bytes() == (
+        b"vendor-bundle-bytes\nexisting-anchor-bytes\nfake-cert-bytes\n"
+    )
+
+
+def test_apply_rebuilds_rhel_trust_store_without_preexisting_bundle(tmp_path) -> None:
+    src = tmp_path / "src"
+    (src / "etc/pki/ca-trust/source/anchors").mkdir(parents=True)
+
+    dst = tmp_path / "dst"
+    context = Context(config=make_config(True), dst=dst, src=src)
+
+    CertificatesModule().apply(context)
+
+    bundle_dst = dst / "etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem"
+    assert bundle_dst.read_bytes() == b"fake-cert-bytes\n"
+
+
+def test_resolve_target_dir_returns_unchanged_when_not_a_symlink(tmp_path) -> None:
+    src = tmp_path / "src"
+    (src / "etc/ssl/certs").mkdir(parents=True)
+    context = Context(config=make_config(True), dst=tmp_path / "dst", src=src)
+
+    assert _resolve_target_dir(context, "etc/ssl/certs") == "etc/ssl/certs"
+
+
+def test_resolve_target_dir_returns_unchanged_without_src(tmp_path) -> None:
+    context = Context(config=make_config(True), dst=tmp_path / "dst", src=None)
+
+    assert _resolve_target_dir(context, "etc/ssl/certs") == "etc/ssl/certs"
+
+
+def test_resolve_target_dir_follows_absolute_symlink(tmp_path) -> None:
+    src = tmp_path / "src"
+    (src / "etc/pki/tls/certs").mkdir(parents=True)
+    (src / "etc/ssl").mkdir(parents=True)
+    (src / "etc/ssl/certs").symlink_to("/etc/pki/tls/certs")
+    context = Context(config=make_config(True), dst=tmp_path / "dst", src=src)
+
+    assert _resolve_target_dir(context, "etc/ssl/certs") == "etc/pki/tls/certs"
+
+
+def test_resolve_target_dir_follows_relative_symlink(tmp_path) -> None:
+    src = tmp_path / "src"
+    (src / "etc/pki/tls/certs").mkdir(parents=True)
+    (src / "etc/ssl").mkdir(parents=True)
+    (src / "etc/ssl/certs").symlink_to("../pki/tls/certs")
+    context = Context(config=make_config(True), dst=tmp_path / "dst", src=src)
+
+    assert _resolve_target_dir(context, "etc/ssl/certs") == "etc/pki/tls/certs"
+
+
+def test_resolve_target_dir_falls_back_when_relative_symlink_escapes_src(
+    tmp_path,
 ) -> None:
-    monkeypatch.setattr(
-        "id_configurator.modules.certificates.subprocess.run",
-        MagicMock(side_effect=FileNotFoundError()),
-    )
-    context = Context(config=make_config(True), dst=tmp_path / "dst", src=None)
+    src = tmp_path / "src"
+    (src / "etc/ssl").mkdir(parents=True)
+    # Escapes past <src> itself via enough ".." components.
+    (src / "etc/ssl/certs").symlink_to("../../../../../outside")
+    context = Context(config=make_config(True), dst=tmp_path / "dst", src=src)
 
-    with pytest.raises(RuntimeError, match="update-ca-certificates is not available"):
-        CertificatesModule().apply(context)
+    assert _resolve_target_dir(context, "etc/ssl/certs") == "etc/ssl/certs"
 
 
-def test_update_ca_certificates_raises_on_failure(tmp_path, monkeypatch) -> None:
-    error = subprocess.CalledProcessError(
-        returncode=1, cmd=["update-ca-certificates"], stderr="boom"
-    )
-    monkeypatch.setattr(
-        "id_configurator.modules.certificates.subprocess.run",
-        MagicMock(side_effect=error),
-    )
-    context = Context(config=make_config(True), dst=tmp_path / "dst", src=None)
+def test_apply_writes_bundle_to_rhel_style_symlinked_etccertsdir(tmp_path) -> None:
+    src = tmp_path / "src"
+    (src / "etc/pki/tls/certs").mkdir(parents=True)
+    (src / "etc/ssl").mkdir(parents=True)
+    (src / "etc/ssl/certs").symlink_to("/etc/pki/tls/certs")
 
-    with pytest.raises(RuntimeError, match="update-ca-certificates failed"):
-        CertificatesModule().apply(context)
+    dst = tmp_path / "dst"
+    context = Context(config=make_config(True), dst=dst, src=src)
+
+    CertificatesModule().apply(context)
+
+    assert not (dst / "etc/ssl/certs").exists()
+    bundle = dst / "etc/pki/tls/certs/ca-certificates.crt"
+    assert bundle.read_bytes() == b"fake-cert-bytes\n"
+    pem = dst / "etc/pki/tls/certs/new-root-ca.pem"
+    assert pem.is_symlink()
+    # /usr/lib/ssl/cert.pem is Debian/Ubuntu-specific: not OpenSSL's default
+    # CAfile on this (RHEL-style) system, so it must not be created.
+    assert not (dst / "usr/lib/ssl/cert.pem").exists()

tests/test_cli.py

@@ -1,5 +1,4 @@
 import json
-import subprocess
 from unittest.mock import MagicMock
 
 from typer.testing import CliRunner
@@ -66,14 +65,7 @@ def test_apply_skips_irrelevant_modules(tmp_path, caplog) -> None:
     assert "skipping module python" in caplog.text
 
 
-def test_apply_runs_relevant_module(tmp_path, monkeypatch) -> None:
-    mock_run = MagicMock(
-        return_value=subprocess.CompletedProcess(
-            args=[], returncode=0, stdout="", stderr=""
-        )
-    )
-    monkeypatch.setattr("id_configurator.modules.certificates.subprocess.run", mock_run)
-
+def test_apply_runs_relevant_module(tmp_path) -> None:
     config_path = write_config(tmp_path, CONFIG_WITH_CERT)
     dst = tmp_path / "dst"
     result = runner.invoke(
@@ -82,7 +74,7 @@ def test_apply_runs_relevant_module(tmp_path, monkeypatch) -> None:
 
     assert result.exit_code == 0
     assert (dst / "usr/local/share/ca-certificates/my-ca.crt").read_bytes() == b"fake"
-    mock_run.assert_called_once()
+    assert (dst / "etc/ssl/certs/ca-certificates.crt").read_bytes() == b"fake\n"
 
 
 def test_main_default_name_calls_app(monkeypatch) -> None:

tests/test_java.py

@@ -122,8 +122,11 @@ def test_apply_adds_certificate_to_pkcs12_and_jks_keystores(tmp_path) -> None:
 
     JavaModule().apply(context)
 
+    # The written truststore's trust-only entries are unencrypted (matching
+    # the JDK's own cacerts), so they load with no password at all - the
+    # password a caller would use for a source-of-truth JDK-style store.
     pkcs12_result = pkcs12.load_pkcs12(
-        (dst / "usr/lib/jvm/java-21/lib/security/cacerts").read_bytes(), b"changeit"
+        (dst / "usr/lib/jvm/java-21/lib/security/cacerts").read_bytes(), None
     )
     pkcs12_aliases = {entry.friendly_name for entry in pkcs12_result.additional_certs}
     assert pkcs12_aliases == {b"already-trusted-ca", b"interdiode-root-ca"}

tox.ini

@@ -106,7 +106,7 @@ commands =
 dockerfile = {tox_root}/tests/dockerfiles/repos/yum-repo.Dockerfile
 expose =
     YUM_REPO_PORT=8443/tcp
-healthcheck_cmd = wget -qO- http://127.0.0.1:8443/repodata/repomd.xml || exit 1
+healthcheck_cmd = wget --no-check-certificate -qO- https://127.0.0.1:8443/repodata/repomd.xml || exit 1
 healthcheck_interval = 1
 healthcheck_retries = 30
 healthcheck_timeout = 2
@@ -128,7 +128,7 @@ commands =
 dockerfile = {tox_root}/tests/dockerfiles/repos/apk-repo.Dockerfile
 expose =
     APK_REPO_PORT=8443/tcp
-healthcheck_cmd = wget -qO- http://127.0.0.1:8443/APKINDEX.tar.gz || exit 1
+healthcheck_cmd = wget --no-check-certificate -qO- https://127.0.0.1:8443/APKINDEX.tar.gz || exit 1
 healthcheck_interval = 1
 healthcheck_retries = 30
 healthcheck_timeout = 2
@@ -159,7 +159,7 @@ commands =
 dockerfile = {tox_root}/tests/dockerfiles/repos/java-repo.Dockerfile
 expose =
     JAVA_REPO_PORT=8443/tcp
-healthcheck_cmd = wget -qO- http://127.0.0.1:8443/org/interdiode/idconfiguratortestpkg/0.0.1/idconfiguratortestpkg-0.0.1.pom || exit 1
+healthcheck_cmd = wget --no-check-certificate -qO- https://127.0.0.1:8443/org/interdiode/idconfiguratortestpkg/0.0.1/idconfiguratortestpkg-0.0.1.pom || exit 1
 healthcheck_interval = 1
 healthcheck_retries = 30
 healthcheck_timeout = 2