Regression tests, envctl, and bug fixes (#13)

* Found too many bugs

* Implements a regression test
* Moves and completely refactors the envctl code
* Allows the user to keep @STR@ values in output files (if you want full control over where external packages comes from post-build)
* Fixes wording in a few places
* envctl redaction is not implemented yet. The original redaction code hasn't been modified.

* Use generic.ini instead of bare_minimum.ini

11 files changed, 500 insertions, 126 deletions

diff --git a/README.md b/README.md
index baa0864..14cd650 100644
--- a/README.md
+++ b/README.md
@@ -141,80 +141,83 @@ stasis mydelivery.ini
 
 # Configuration
 
-## Environment variables
-
-| Name                                      | Purpose                                                                 | 
-|-------------------------------------------|-------------------------------------------------------------------------|
-| TMPDIR                                    | Change default path to store temporary data                             |
-| STASIS_ROOT                               | Change default path to write STASIS's data                              |
-| STASIS_SYSCONFDIR                         | Change default path to search for configuration files                   | 
-| STASIS_CPU_COUNT<br/>(alias: CPU_COUNT)   | Number of available CPUs                                                |
-| STASIS_GH_TOKEN<br/>(alias: GITHUB_TOKEN) | GitHub API token<br/>(Scope: "Contents" repository permissions (write)) |
-| STASIS_JF_ARTIFACTORY_URL                 | Artifactory service URL (ending in `/artifactory`)                      | 
-| STASIS_JF_ACCESS_TOKEN                    | Artifactory Access Token                                                | 
-| STASIS_JF_USER                            | Artifactory username                                                    | 
-| STASIS_JF_PASSWORD                        | Artifactory password                                                    | 
-| STASIS_JF_SSH_KEY_PATH                    | Path to SSH public key file                                             |
-| STASIS_JF_SSH_PASSPHRASE                  | Password associated with SSH public key file                            | 
-| STASIS_JF_CLIENT_CERT_CERT_PATH           | Path to OpenSSL cert files                                              | 
-| STASIS_JF_CLIENT_CERT_KEY_PATH            | OpenSSL key file (in cert path)                                         | 
-| STASIS_JF_REPO                            | Artifactory "generic" repository to write to                            | 
-
-# Variable expansion
-
-## Template strings
-
-Template strings can be accessed using the `{{ subject.key }}` notation in any STASIS configuration file.
-
-| Name                        | Purpose                                                                                                                 |
-|-----------------------------|-------------------------------------------------------------------------------------------------------------------------|
-| meta.name                   | Delivery name                                                                                                           |
-| meta.version                | Delivery version                                                                                                        |
-| meta.codename               | Delivery codename                                                                                                       |
-| meta.mission                | Delivery mission                                                                                                        |
-| meta.python                 | Python version (e.g. 3.11)                                                                                              |
-| meta.python_compact         | Python (e.g. 311)                                                                                                       |
-| info.time_str_epoch         | UNIX Epoch timestamp                                                                                                    |
-| info.release_name           | Rendered delivery release name                                                                                          |
-| info.build_name             | Rendered delivery build name                                                                                            |
-| info.build_number           | Rendered delivery build number                                                                                          |
-| storage.tmpdir              | Ohymcal temp directory                                                                                                  |
-| storage.delivery_dir        | STASIS delivery output directory                                                                                        |
-| storage.results_dir         | STASIS test results directory                                                                                           |
-| storage.conda_artifact_dir  | STASIS conda package directory                                                                                          |
-| storage.wheel_artifact_dir  | STASIS wheel package directory                                                                                          |
-| storage.build_sources_dir   | STASIS sources directory                                                                                                |
-| storage.build_docker_dir    | STASIS docker directory                                                                                                 |
-| conda.installer_name        | Conda distribution name                                                                                                 |
-| conda.installer_version     | Conda distribution version                                                                                              |
-| conda.installer_platform    | Conda target platform                                                                                                   |
-| conda.installer_arch        | Conda target architecture                                                                                               |
-| conda.installer_baseurl     | Conda installer URL                                                                                                     |
-| system.arch                 | System CPU Architecture                                                                                                 |
-| system.platform             | System Platform (OS)                                                                                                    |
-| deploy.docker.registry      | Docker registry                                                                                                         |
-| deploy.jfrog.repo           | Artifactory destination repository                                                                                      |
-| workaround.tox_posargs      | Return populated `-c` and `--root` tox arguments.<br/>Force-enables positional arguments in tox's command line parser.  |
-| workaround.conda_reactivate | Reinitialize the conda runtime environment.<br/>Use this after calling `conda install` from within a `[test:*].script`. |
+## Command Line Options
+
+| Long Option         | Short Option | Purpose                                                        |
+|:--------------------|:------------:|:---------------------------------------------------------------|
+| --help              |      -h      | Display usage statement                                        |
+| --version           |      -V      | Display program version                                        |
+| --continue-on-error |      -C      | Allow tests to fail                                            |
+| --config ARG        |    -c ARG    | Read STASIS configuration file                                 |
+| --python ARG        |    -p ARG    | Override version of Python in configuration                    |
+| --verbose           |      -v      | Increase output verbosity                                      |
+| --unbuffered        |      -U      | Disable line buffering                                         |
+| --update-base       |     n/a      | Update conda installation prior to STATIS environment creation |
+| --overwrite         |     n/a      | Overwrite an existing release                                  |
+| --no-docker         |     n/a      | Do not build docker images                                     |
+| --no-artifactory    |     n/a      | Do not upload artifacts to Artifactory                         |
+| --no-testing        |     n/a      | Do not execute test scripts                                    |
+| --no-rewrite        |     n/a      | Do not rewrite paths and URLs in output files                  |
+| DELIVERY_FILE       |     n/a      | STASIS delivery file                                           |
 
-The template engine also provides an interface to environment variables using the `{{ env:VARIABLE_NAME }}` notation.
 
-```ini
-[meta]
-name = {{ env:MY_DYNAMIC_DELIVERY_NAME }}
-version = {{ env:MY_DYNAMIC_DELIVERY_VERSION }}
-python = {{ env:MY_DYNAMIC_PYTHON_VERSION }}
-```
-
-## Template Functions
 
-Template functions can be accessed using the `{{ func:NAME(ARG,...) }}` notation.
-
-| Name                          | Purpose                                      |
-|-------------------------------|----------------------------------------------|
-| get_github_release_notes_auto | Generate release notes for all test contexts |
+## Environment variables
 
-# Delivery files
+| Name                            | Purpose                                                                 | 
+|---------------------------------|-------------------------------------------------------------------------|
+| TMPDIR                          | Change default path to store temporary data                             |
+| STASIS_ROOT                     | Change default path to write STASIS's data                              |
+| STASIS_SYSCONFDIR               | Change default path to search for configuration files                   | 
+| STASIS_CPU_COUNT                | Number of available CPUs                                                |
+| STASIS_GH_TOKEN                 | GitHub API token<br/>(Scope: "Contents" repository permissions (write)) |
+| STASIS_JF_ARTIFACTORY_URL       | Artifactory service URL (ending in `/artifactory`)                      | 
+| STASIS_JF_ACCESS_TOKEN          | Artifactory Access Token                                                | 
+| STASIS_JF_USER                  | Artifactory username                                                    | 
+| STASIS_JF_PASSWORD              | Artifactory password                                                    | 
+| STASIS_JF_SSH_KEY_PATH          | Path to SSH public key file                                             |
+| STASIS_JF_SSH_PASSPHRASE        | Password associated with SSH public key file                            | 
+| STASIS_JF_CLIENT_CERT_CERT_PATH | Path to OpenSSL cert files                                              | 
+| STASIS_JF_CLIENT_CERT_KEY_PATH  | OpenSSL key file (in cert path)                                         | 
+| STASIS_JF_REPO                  | Artifactory "generic" repository to write to                            | 
+
+## Main configuration (stasis.ini)
+
+The default path to the configuration file is `[CMAKE_INSTALL_PREFIX]/etc/stasis/stasis.ini`. You may override this by setting the `STASIS_SYSCONFDIR` environment variable to a path that points elsewhere. 
+
+### Sections
+
+#### default 
+
+| Name                           |  Type   | Purpose                                                              |
+|--------------------------------|:-------:|----------------------------------------------------------------------|
+| continue_on_error              | Boolean | Keep going even if a test fails                                      |
+| always_update_base_environment | Boolean | Update all packages in the base to the latest release                |
+| conda_fresh_start              | Boolean | Remove conda installation during initialization                      |
+| conda_install_prefix           | String  | Install conda in a custom prefix path                                |
+| conda_packages                 |  List   | Conda packages to be installed/overridden in the `base` environment  |
+| pip_packages                   |  List   | Python packages to be installed/overridden in the `base` environment |
+| conda_staging_url              | String  | URL to conda channel                                                 |
+
+### jfrog_cli_download
+
+| Name           |  Type  | Purpose                                                               |
+|----------------|:------:|-----------------------------------------------------------------------|
+| url            | String | Base URL of JFrog CLI release server                                  |
+| project        | String | Product identifier (i.e. `jfrog-cli`)                                 |
+| version_series | String | Product version series (i.e. `v2-jf`)                                 |
+| version        | String | Product version to install. `[RELEASE]` downloads the latest version. |
+| filename       | String | Product file name (i.e. `jf`)                                         |
+
+### deploy:artifactory
+
+| Name |  Type  | Purpose                                              |
+|------|:------:|------------------------------------------------------|
+| url  | String | Set artifactory service URL (ending in /artifactory) |
+| repo | String | Set artifactory repository                           |
+
+
+# Delivery configuration
 
 ## Sections
 
@@ -285,6 +288,60 @@ The `deploy:docker` section controls how Docker images are created, when a `Dock
 | image_compression | String | Compression program (with arguments)         | N        |
 | build_args        | List   | Values passed to `docker build --build-args` | N        |
 | tags              | List   | Docker image tag(s)                          | Y        |
+# Variable expansion
+
+## Template strings
+
+Template strings can be accessed using the `{{ subject.key }}` notation in any STASIS configuration file.
+
+| Name                        | Purpose                                                                                                                 |
+|-----------------------------|-------------------------------------------------------------------------------------------------------------------------|
+| meta.name                   | Delivery name                                                                                                           |
+| meta.version                | Delivery version                                                                                                        |
+| meta.codename               | Delivery codename                                                                                                       |
+| meta.mission                | Delivery mission                                                                                                        |
+| meta.python                 | Python version (e.g. 3.11)                                                                                              |
+| meta.python_compact         | Python (e.g. 311)                                                                                                       |
+| info.time_str_epoch         | UNIX Epoch timestamp                                                                                                    |
+| info.release_name           | Rendered delivery release name                                                                                          |
+| info.build_name             | Rendered delivery build name                                                                                            |
+| info.build_number           | Rendered delivery build number                                                                                          |
+| storage.tmpdir              | Ohymcal temp directory                                                                                                  |
+| storage.delivery_dir        | STASIS delivery output directory                                                                                        |
+| storage.results_dir         | STASIS test results directory                                                                                           |
+| storage.conda_artifact_dir  | STASIS conda package directory                                                                                          |
+| storage.wheel_artifact_dir  | STASIS wheel package directory                                                                                          |
+| storage.build_sources_dir   | STASIS sources directory                                                                                                |
+| storage.build_docker_dir    | STASIS docker directory                                                                                                 |
+| conda.installer_name        | Conda distribution name                                                                                                 |
+| conda.installer_version     | Conda distribution version                                                                                              |
+| conda.installer_platform    | Conda target platform                                                                                                   |
+| conda.installer_arch        | Conda target architecture                                                                                               |
+| conda.installer_baseurl     | Conda installer URL                                                                                                     |
+| system.arch                 | System CPU Architecture                                                                                                 |
+| system.platform             | System Platform (OS)                                                                                                    |
+| deploy.docker.registry      | Docker registry                                                                                                         |
+| deploy.jfrog.repo           | Artifactory destination repository                                                                                      |
+| workaround.tox_posargs      | Return populated `-c` and `--root` tox arguments.<br/>Force-enables positional arguments in tox's command line parser.  |
+| workaround.conda_reactivate | Reinitialize the conda runtime environment.<br/>Use this after calling `conda install` from within a `[test:*].script`. |
+
+The template engine also provides an interface to environment variables using the `{{ env:VARIABLE_NAME }}` notation.
+
+```ini
+[meta]
+name = {{ env:MY_DYNAMIC_DELIVERY_NAME }}
+version = {{ env:MY_DYNAMIC_DELIVERY_VERSION }}
+python = {{ env:MY_DYNAMIC_PYTHON_VERSION }}
+```
+
+## Template Functions
+
+Template functions can be accessed using the `{{ func:NAME(ARG,...) }}` notation.
+
+| Name                          | Purpose                                      |
+|-------------------------------|----------------------------------------------|
+| get_github_release_notes_auto | Generate release notes for all test contexts |
+
 
 # Mission files
 
diff --git a/include/core.h b/include/core.h
index d065096..1ea0f5e 100644
--- a/include/core.h
+++ b/include/core.h
@@ -21,6 +21,7 @@
 #define HTTP_ERROR(X) X >= 400
 
 #include "config.h"
+#include "envctl.h"
 #include "template.h"
 #include "utils.h"
 #include "copy.h"
@@ -59,11 +60,6 @@
         } \
     } while (0)
 
-struct EnvCtl {
-    unsigned flags;
-    const char *name[10];
-};
-
 struct STASIS_GLOBAL {
     bool verbose; //!< Enable verbose output
     bool always_update_base_environment; //!< Update base environment immediately after activation
@@ -73,6 +69,7 @@ struct STASIS_GLOBAL {
     bool enable_artifactory; //!< Enable artifactory uploads
     bool enable_testing; //!< Enable package testing
     bool enable_overwrite; //!< Enable release file clobbering
+    bool enable_rewrite_spec_stage_2; //!< Enable automatic @STR@ replacement in output files
     struct StrList *conda_packages; //!< Conda packages to install after initial activation
     struct StrList *pip_packages; //!< Pip packages to install after initial activation
     char *tmpdir; //!< Path to temporary storage directory
@@ -93,13 +90,10 @@ struct STASIS_GLOBAL {
         char *repo;
         char *url;
     } jfrog;
-    struct EnvCtl envctl[];
+    struct EnvCtl *envctl;
 };
 extern struct STASIS_GLOBAL globals;
 
-#define STASIS_ENVCTL_PASSTHRU 0 << 1
-#define STASIS_ENVCTL_REQUIRED 1 << 1
-#define STASIS_ENVCTL_REDACT 2 << 1
 extern const char *VERSION;
 extern const char *AUTHOR;
 extern const char *BANNER;
diff --git a/include/envctl.h b/include/envctl.h
new file mode 100644
index 0000000..c8ef357
--- /dev/null
+++ b/include/envctl.h
@@ -0,0 +1,37 @@
+#ifndef STASIS_ENVCTL_H
+#define STASIS_ENVCTL_H
+
+#include <stdlib.h>
+
+#define STASIS_ENVCTL_PASSTHRU 0
+#define STASIS_ENVCTL_REQUIRED 1 << 1
+#define STASIS_ENVCTL_REDACT 1 << 2
+#define STASIS_ENVCTL_DEFAULT_ALLOC 100
+
+#define STASIS_ENVCTL_RET_FAIL (-1)
+#define STASIS_ENVCTL_RET_SUCCESS 1
+#define STASIS_ENVCTL_RET_IGNORE 2
+typedef int (envctl_except_fn)(const void *, const void *);
+
+struct EnvCtl_Item {
+    unsigned flags; //<! One or more STASIS_ENVCTL_* flags
+    const char *name; //<! Environment variable name
+    envctl_except_fn *callback;
+};
+
+struct EnvCtl {
+    size_t num_alloc;
+    size_t num_used;
+    struct EnvCtl_Item **item;
+};
+
+struct EnvCtl *envctl_init();
+int envctl_register(struct EnvCtl **envctl, unsigned flags, envctl_except_fn *callback, const char *name);
+unsigned envctl_get_flags(const struct EnvCtl *envctl, const char *name);
+unsigned envctl_check_required(unsigned flags);
+unsigned envctl_check_redact(unsigned flags);
+int envctl_check_present(const struct EnvCtl_Item *item, const char *name);
+void envctl_do_required(const struct EnvCtl *envctl, int verbose);
+void envctl_free(struct EnvCtl **envctl);
+
+#endif // STASIS_ENVCTL_H
\ No newline at end of file
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a7b06f7..2399dc5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -24,6 +24,7 @@ add_library(stasis_core STATIC
         junitxml.c
         github.c
         template_func_proto.c
+        envctl.c
 )
 
 add_executable(stasis
diff --git a/src/delivery.c b/src/delivery.c
index b27ab08..d7b9b99 100644
--- a/src/delivery.c
+++ b/src/delivery.c
@@ -1676,7 +1676,7 @@ void delivery_rewrite_spec(struct Delivery *ctx, char *filename, unsigned stage)
         }
         remove(tempfile);
         guard_free(tempfile);
-    } else if (stage == DELIVERY_REWRITE_SPEC_STAGE_2) {
+    } else if (globals.enable_rewrite_spec_stage_2 && stage == DELIVERY_REWRITE_SPEC_STAGE_2) {
         // Replace "local" channel with the staging URL
         if (ctx->storage.conda_staging_url) {
             file_replace_text(filename, "@CONDA_CHANNEL@", ctx->storage.conda_staging_url, 0);
@@ -1684,15 +1684,19 @@ void delivery_rewrite_spec(struct Delivery *ctx, char *filename, unsigned stage)
             sprintf(output, "%s/%s/%s/%s/packages/conda", globals.jfrog.url, globals.jfrog.repo, ctx->meta.mission, ctx->info.build_name);
             file_replace_text(filename, "@CONDA_CHANNEL@", output, 0);
         } else {
-            msg(STASIS_MSG_WARN, "conda_staging_url is not configured\n", filename);
-            file_replace_text(filename, "  - @CONDA_CHANNEL@", "", 0);
+            msg(STASIS_MSG_WARN, "conda_staging_dir is not configured. Using fallback: '%s'\n", ctx->storage.conda_artifact_dir);
+            file_replace_text(filename, "@CONDA_CHANNEL@", ctx->storage.conda_artifact_dir, 0);
         }
 
         if (ctx->storage.wheel_staging_url) {
             file_replace_text(filename, "@PIP_ARGUMENTS@", ctx->storage.wheel_staging_url, 0);
-        } else if (globals.jfrog.repo) {
+        } else if (globals.jfrog.url && globals.jfrog.repo) {
             sprintf(output, "--extra-index-url %s/%s/%s/%s/packages/wheels", globals.jfrog.url, globals.jfrog.repo, ctx->meta.mission, ctx->info.build_name);
             file_replace_text(filename, "@PIP_ARGUMENTS@", output, 0);
+        } else {
+            msg(STASIS_MSG_WARN, "wheel_staging_dir is not configured. Using fallback: '%s'\n", ctx->storage.wheel_artifact_dir);
+            sprintf(output, "--extra-index-url file://%s", ctx->storage.wheel_artifact_dir);
+            file_replace_text(filename, "@PIP_ARGUMENTS@", output, 0);
         }
     }
 }
diff --git a/src/envctl.c b/src/envctl.c
new file mode 100644
index 0000000..78dd760
--- /dev/null
+++ b/src/envctl.c
@@ -0,0 +1,125 @@
+#include "envctl.h"
+#include "core.h"
+
+struct EnvCtl *envctl_init() {
+    struct EnvCtl *result;
+
+    result = calloc(1, sizeof(*result));
+    if (!result) {
+        return NULL;
+    }
+
+    result->num_alloc = STASIS_ENVCTL_DEFAULT_ALLOC;
+    result->item = calloc(result->num_alloc + 1, sizeof(result->item));
+    if (!result->item) {
+        guard_free(result);
+        return NULL;
+    }
+
+    return result;
+}
+
+static int callback_builtin_nop(const void *a, const void *b) {
+    return STASIS_ENVCTL_RET_SUCCESS;
+}
+
+int envctl_register(struct EnvCtl **envctl, unsigned flags, envctl_except_fn *callback, const char *name) {
+    if ((*envctl)->num_used == (*envctl)->num_alloc) {
+        (*envctl)->num_alloc += STASIS_ENVCTL_DEFAULT_ALLOC;
+        struct EnvCtl_Item **tmp = realloc((*envctl)->item, (*envctl)->num_alloc + 1 * sizeof((*envctl)->item));
+        if (!tmp) {
+            return 1;
+        } else {
+            (*envctl)->item = tmp;
+        }
+    }
+
+    struct EnvCtl_Item **item = (*envctl)->item;
+    item[(*envctl)->num_used] = calloc(1, sizeof(*item[0]));
+    if (!item[(*envctl)->num_used]) {
+        return 1;
+    }
+    if (!callback) {
+        callback = &callback_builtin_nop;
+    }
+    item[(*envctl)->num_used]->callback = callback;
+    item[(*envctl)->num_used]->name = name;
+    item[(*envctl)->num_used]->flags = flags;
+
+    (*envctl)->num_used++;
+    return 0;
+}
+
+size_t envctl_get_index(const struct EnvCtl *envctl, const char *name) {
+    for (size_t i = 0; i < envctl->num_used; i++) {
+        if (!strcmp(envctl->item[i]->name, name)) {
+            // pack state flag, outer (struct) index and inner (name) index
+            return 1L << 63L | i;
+        }
+    }
+    return 0;
+}
+
+void envctl_decode_index(size_t in_i, size_t *state, size_t *out_i, size_t *name_i) {
+    *state = ((in_i >> 63L) & 1);
+    *out_i = in_i & 0xffffffffL;
+}
+
+unsigned envctl_check_required(unsigned flags) {
+    return flags & STASIS_ENVCTL_REQUIRED;
+}
+
+unsigned envctl_check_redact(unsigned flags) {
+    return flags & STASIS_ENVCTL_REDACT;
+}
+
+int envctl_check_present(const struct EnvCtl_Item *item, const char *name) {
+    return ((!strcmp(item->name, name)) && getenv(name)) ? 1 : 0;
+}
+
+unsigned envctl_get_flags(const struct EnvCtl *envctl, const char *name) {
+    size_t poll_index = envctl_get_index(envctl, name);
+    size_t id = 0;
+    size_t name_id = 0;
+    size_t state = 0;
+    envctl_decode_index(poll_index, &state, &id, &name_id);
+    if (!state) {
+        return 0;
+    } else {
+        fprintf(stderr, "managed environment variable: %s\n", name);
+    }
+    return envctl->item[id]->flags;
+}
+
+void envctl_do_required(const struct EnvCtl *envctl, int verbose) {
+    for (size_t i = 0; i < envctl->num_used; i++) {
+        struct EnvCtl_Item *item = envctl->item[i];
+        const char *name = item->name;
+        envctl_except_fn *callback = item->callback;
+
+        if (verbose) {
+            msg(STASIS_MSG_L2, "Verifying %s\n", name);
+        }
+        int code = callback((const void *) item, (const void *) name);
+        if (code == STASIS_ENVCTL_RET_IGNORE || code == STASIS_ENVCTL_RET_SUCCESS) {
+            continue;
+        } else if (code == STASIS_ENVCTL_RET_FAIL) {
+            fprintf(stderr, "\n%s must be set. Exiting.\n", name);
+            exit(1);
+        } else {
+            fprintf(stderr, "\nan unknown envctl callback code occurred: %d\n", code);
+            exit(1);
+        }
+    }
+}
+
+void envctl_free(struct EnvCtl **envctl) {
+    if (!envctl) {
+        return;
+    }
+    for (size_t i = 0; i < (*envctl)->num_used; i++) {
+        guard_free((*envctl)->item[i]);
+    }
+    guard_free((*envctl)->item);
+    guard_free(*envctl);
+}
\ No newline at end of file
diff --git a/src/globals.c b/src/globals.c
index 18a32b5..5fdf05d 100644
--- a/src/globals.c
+++ b/src/globals.c
@@ -36,22 +36,7 @@ struct STASIS_GLOBAL globals = {
         .enable_docker = true,
         .enable_artifactory = true,
         .enable_testing = true,
-        .envctl = {
-            {.flags = STASIS_ENVCTL_PASSTHRU, .name = {"TMPDIR", NULL}},
-            {.flags = STASIS_ENVCTL_PASSTHRU, .name = {"STASIS_ROOT", NULL}},
-            {.flags = STASIS_ENVCTL_PASSTHRU, .name = {"STASIS_SYSCONFDIR", NULL}},
-            {.flags = STASIS_ENVCTL_PASSTHRU, .name = {"STASIS_CPU_COUNT", "CPU_COUNT", NULL}},
-            {.flags = STASIS_ENVCTL_REQUIRED | STASIS_ENVCTL_REDACT, .name={"STASIS_GH_TOKEN", "GITHUB_TOKEN", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_ACCESS_TOKEN", NULL}},
-            {.flags = STASIS_ENVCTL_PASSTHRU, .name = {"STASIS_JF_USER", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_PASSWORD", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_SSH_KEY_PATH", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_SSH_PASSPHRASE", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_CLIENT_CERT_CERT_PATH", NULL}},
-            {.flags = STASIS_ENVCTL_REDACT, .name = {"STASIS_JF_CLIENT_CERT_KEY_PATH", NULL}},
-            {.flags = STASIS_ENVCTL_REQUIRED, .name = {"STASIS_JF_REPO", NULL}},
-            {.flags = 0, .name = {NULL}},
-        }
+        .enable_rewrite_spec_stage_2 = true,
 };
 
 void globals_free() {
@@ -71,4 +56,7 @@ void globals_free() {
     guard_free(globals.jfrog.remote_filename);
     guard_free(globals.workaround.tox_posargs);
     guard_free(globals.workaround.conda_reactivate);
+    if (globals.envctl) {
+        envctl_free(&globals.envctl);
+    }
 }
diff --git a/src/stasis_main.c b/src/stasis_main.c
index 9348140..7e2262a 100644
--- a/src/stasis_main.c
+++ b/src/stasis_main.c
@@ -10,6 +10,7 @@
 #define OPT_NO_ARTIFACTORY 1002
 #define OPT_NO_TESTING 1003
 #define OPT_OVERWRITE 1004
+#define OPT_NO_REWRITE_SPEC_STAGE_2 1005
 static struct option long_options[] = {
         {"help", no_argument, 0, 'h'},
         {"version", no_argument, 0, 'V'},
@@ -23,6 +24,7 @@ static struct option long_options[] = {
         {"no-docker", no_argument, 0, OPT_NO_DOCKER},
         {"no-artifactory", no_argument, 0, OPT_NO_ARTIFACTORY},
         {"no-testing", no_argument, 0, OPT_NO_TESTING},
+        {"no-rewrite", no_argument, 0, OPT_NO_REWRITE_SPEC_STAGE_2},
         {0, 0, 0, 0},
 };
 
@@ -39,6 +41,7 @@ const char *long_options_help[] = {
         "Do not build docker images",
         "Do not upload artifacts to Artifactory",
         "Do not execute test scripts",
+        "Do not rewrite paths and URLs in output files",
         NULL,
 };
 
@@ -98,36 +101,53 @@ static void usage(char *progname) {
     }
 }
 
-static int get_envctl_key_index_(size_t i) {
-    for (int x = 0; x < (int)(sizeof(globals.envctl[i].name) / sizeof(*globals.envctl[i].name)); x++) {
-        const char *name = globals.envctl[i].name[x];
-        if (!name) {
-            return -1;
-        }
-        const char *data = getenv(name);
-        if (data != NULL) {
-            return x;
+static int callback_except_jf(const void *a, const void *b) {
+    const struct EnvCtl_Item *item = a;
+    const char *name = b;
+
+    if (!globals.enable_artifactory) {
+        return STASIS_ENVCTL_RET_IGNORE;
+    }
+
+    if (envctl_check_required(item->flags)) {
+        const char *content = getenv(name);
+        if (!content || isempty((char *) content)) {
+            return STASIS_ENVCTL_RET_FAIL;
         }
     }
-    return -1;
+
+    return STASIS_ENVCTL_RET_SUCCESS;
+}
+
+static int callback_except_gh(const void *a, const void *b) {
+    const struct EnvCtl_Item *item = a;
+    const char *name = b;
+    //printf("GH exception check: %s\n", name);
+    if (envctl_check_required(item->flags) && envctl_check_present(item, name)) {
+        return STASIS_ENVCTL_RET_SUCCESS;
+    }
+
+    return STASIS_ENVCTL_RET_FAIL;
 }
 
 static void check_system_env_requirements() {
     msg(STASIS_MSG_L1, "Checking environment\n");
-    for (size_t i = 0; globals.envctl[i].name[0] != NULL; i++) {
-        unsigned int flags = globals.envctl[i].flags;
-        int key = get_envctl_key_index_(i);
-        if (key < 0) {
-            if (flags & STASIS_ENVCTL_REQUIRED) {
-                if (!strcmp(globals.envctl[i].name[0], "STASIS_JF_REPO") && !globals.enable_artifactory) {
-                    continue;
-                }
-                msg(STASIS_MSG_L2 | STASIS_MSG_ERROR, "Environment variable '%s' must be defined.\n",
-                    globals.envctl[i].name[0]);
-                exit(1);
-            }
-        }
-    }
+    globals.envctl = envctl_init();
+    envctl_register(&globals.envctl, STASIS_ENVCTL_PASSTHRU, NULL, "TMPDIR");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_PASSTHRU, NULL, "STASIS_ROOT");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_PASSTHRU, NULL, "STASIS_SYSCONFDIR");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_PASSTHRU, NULL, "STASIS_CPU_COUNT");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REQUIRED | STASIS_ENVCTL_REDACT, callback_except_gh, "STASIS_GH_TOKEN");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REQUIRED, callback_except_jf, "STASIS_JF_ARTIFACTORY_URL");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_ACCESS_TOKEN");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_PASSTHRU, NULL, "STASIS_JF_USER");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_PASSWORD");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_SSH_KEY_PATH");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_SSH_PASSPHRASE");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_CLIENT_CERT_CERT_PATH");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REDACT, NULL, "STASIS_JF_CLIENT_CERT_KEY_PATH");
+    envctl_register(&globals.envctl, STASIS_ENVCTL_REQUIRED, callback_except_jf, "STASIS_JF_REPO");
+    envctl_do_required(globals.envctl, globals.verbose);
 }
 
 static void check_system_requirements(struct Delivery *ctx) {
@@ -244,6 +264,9 @@ int main(int argc, char *argv[]) {
             case OPT_NO_TESTING:
                 globals.enable_testing = false;
                 break;
+            case OPT_NO_REWRITE_SPEC_STAGE_2:
+                globals.enable_rewrite_spec_stage_2 = false;
+                break;
             case '?':
             default:
                 exit(1);
@@ -649,10 +672,10 @@ int main(int argc, char *argv[]) {
             msg(STASIS_MSG_L1, "Uploading artifacts\n");
             delivery_artifact_upload(&ctx);
         } else {
-            msg(STASIS_MSG_L1 | STASIS_MSG_WARN, "Artifact uploading is disabled\n");
+            msg(STASIS_MSG_L1 | STASIS_MSG_WARN, "Artifactory upload is disabled by CLI argument\n");
         }
     } else {
-        msg(STASIS_MSG_L1 | STASIS_MSG_WARN, "Artifact uploading is disabled. deploy:artifactory is not configured\n");
+        msg(STASIS_MSG_L1 | STASIS_MSG_WARN, "Artifactory upload is disabled. deploy:artifactory is not configured\n");
     }
 
     msg(STASIS_MSG_L1, "Cleaning up\n");
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index f3a45e8..f06638e 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -2,15 +2,20 @@ include_directories(
         ${CMAKE_SOURCE_DIR}/include
         ${CMAKE_BINARY_DIR}/include
 )
+find_program(BASH_PROGRAM bash)
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/tests)
 set(CTEST_BINARY_DIRECTORY ${PROJECT_BINARY_DIR}/tests)
 set(nix_gnu_cflags -Wno-error -Wno-unused-parameter -Wno-discarded-qualifiers)
 set(nix_clang_cflags -Wno-unused-parameter -Wno-incompatible-pointer-types-discards-qualifiers)
 set(win_msvc_cflags /Wall)
 
-
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/data/generic.ini ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
 file(GLOB files "test_*.c")
 
+if (BASH_PROGRAM)
+    add_test (rt_generic ${BASH_PROGRAM} ${CMAKE_CURRENT_SOURCE_DIR}/rt_generic.sh)
+endif()
+
 foreach(file ${files})
     string(REGEX REPLACE "(^.*/|\\.[^.]*$)" "" file_without_ext ${file})
     add_executable(${file_without_ext} ${file})
@@ -29,4 +34,6 @@ foreach(file ${files})
     set_tests_properties(${file_without_ext}
             PROPERTIES
             SKIP_RETURN_CODE 127)
+    set_property(TEST ${file_without_ext}
+            PROPERTY ENVIRONMENT "STASIS_SYSCONFDIR=${CMAKE_SOURCE_DIR}")
 endforeach()
\ No newline at end of file
diff --git a/tests/data/generic.ini b/tests/data/generic.ini
new file mode 100644
index 0000000..ef0180b
--- /dev/null
+++ b/tests/data/generic.ini
@@ -0,0 +1,51 @@
+[meta]
+mission = generic
+name = GENERIC
+version = 1.2.3
+rc = 1
+final = false
+based_on =
+python = 3.11
+
+
+[conda]
+installer_name = Miniforge3
+installer_version = 24.3.0-0
+installer_platform = {{env:STASIS_CONDA_PLATFORM}}
+installer_arch = {{env:STASIS_CONDA_ARCH}}
+installer_baseurl = https://github.com/conda-forge/miniforge/releases/download/{{conda.installer_version}}
+;conda_packages =
+pip_packages =
+    firewatch
+
+
+[runtime]
+PYTHONUNBUFFERED = 1
+
+
+[test:firewatch]
+version = 0.0.4
+repository = https://github.com/astroconda/firewatch
+script =
+    pip install -e '.'
+
+
+[deploy:artifactory:delivery]
+files =
+    {{ storage.output_dir }}/**
+dest = {{ meta.mission }}/{{ info.build_name }}/
+
+
+[deploy:docker]
+;registry = bytesalad.stsci.edu
+image_compression = zstd -v -9 -c
+build_args =
+    SNAPSHOT_INPUT={{ info.release_name }}.yml
+    SNAPSHOT_PKGDIR=packages
+tags =
+    {{ meta.name }}:{{ info.build_number }}-py{{ meta.python_compact }}
+    {{ deploy.docker.registry }}/{{ meta.name }}:{{ info.build_number }}-py{{ meta.python_compact }}
+test_script =
+    source /etc/profile
+    python -m pip freeze
+    mamba info
diff --git a/tests/rt_generic.sh b/tests/rt_generic.sh
new file mode 100644
index 0000000..200f66f
--- /dev/null
+++ b/tests/rt_generic.sh
@@ -0,0 +1,87 @@
+#!/usr/bin/env bash
+set -x
+unset STASIS_SYSCONFDIR
+if [ -n "$GITHUB_TOKEN" ] && [ -z "$STASIS_GH_TOKEN"]; then
+    export STASIS_GH_TOKEN="$GITHUB_TOKEN"
+else
+    export STASIS_GH_TOKEN="anonymous"
+fi
+
+topdir=$(pwd)
+
+ws="rt_workspace"
+mkdir -p "$ws"
+ws="$(realpath $ws)"
+
+prefix="$ws"/local
+mkdir -p "$prefix"
+
+bdir="$ws"/build
+mkdir -p "$bdir"
+
+pushd "$bdir"
+cmake -DCMAKE_INSTALL_PREFIX="$prefix" "${topdir}"/../..
+make install
+export PATH="$prefix/bin:$PATH"
+popd
+
+pushd "$ws"
+    type -P stasis
+    type -P stasis_indexer
+
+    stasis --no-docker --no-artifactory --unbuffered -v "$topdir"/generic.ini
+    retcode=$?
+
+    set +x
+
+    echo "#### Files ####"
+    find stasis/*/output | sort
+    echo
+
+    echo "#### Contents ####"
+    files=$(find stasis/*/output -type f \( -name '*.yml' -o -name '*.md' -o -name '*.stasis' \) | sort)
+    for x in $files; do
+        echo
+        echo "FILENAME: $x"
+        echo
+        cat "$x"
+        echo "[EOF]"
+        echo
+
+        fail_on_main=(
+            "(null)"
+        )
+        for cond in "${fail_on_main[@]}"; do
+            if grep --color -H -n "$cond" "$x" >&2; then
+                echo "ERROR DETECTED IN $x!" >&2
+                retcode=2
+            fi
+        done
+    done
+
+    # Something above failed, so drop out. Don't bother indexing.
+    # Don't clean up either.
+    (( retcode )) && exit $retcode
+
+    fail_on_indexer=(
+        "(null)"
+    )
+    logfile="stasis_indexer.log"
+    set -x
+    stasis_indexer --web --unbuffered -v stasis/* 2>&1 | tee "$logfile"
+
+    set +x
+    find output
+
+    for cond in "${fail_on_indexer[@]}"; do
+        if grep --color -H -n "$cond" "$logfile" >&2; then
+            echo "ERROR DETECTED IN INDEX OPERATION!" >&2
+            exit 1
+        fi
+    done
+
+popd
+
+rm -rf "$ws"
+
+exit $retcode
\ No newline at end of file