Remove extra directory in packages

README.md

@@ -22,7 +22,7 @@ which are pointed to the corresponding vulnerabilities in target files.
 
 * A `fix object` represents a proposed fix for the problem, indicated by tool.\
 It specifies a set of artifacts to modify. For each artifact, it specifies regions to remove, and provides new content to insert.
-* `Fix-Patches`, in its turn will parse such sections, create copy of target files, which are presented in `SARIF`,
+* `Fix-Patches`, in its turn, will parse such sections, create copy of target files, which are presented in `SARIF`,
 and automatically apply fixes to these copies.
 
 The result output will contain the list of paths to the copies of provided target files with applied fixes. 
@@ -32,7 +32,8 @@ The result output will contain the list of paths to the copies of provided targe
 #### How to use:
 
 Library provides easy-to-use API for fix patches applying, it's just need to provide
-the path to `SARIF` file with expected fixes and the list of paths to target files which are presented in `SARIF`.
+the path to `SARIF` file, which contain the list of fixes (`fix objects`) for target files and the list of paths to these files,
+in the manner, in which they are presented in `SARIF` (via absolute/relative paths).
 
 ```kotlin
     val processedFiles: List<Path> = SarifFixAdapter(

fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/cli/adapter/SarifFixAdapter.kt → fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/adapter/SarifFixAdapter.kt

@@ -1,15 +1,15 @@
-package com.saveourtool.sarifutils.cli.adapter
+package com.saveourtool.sarifutils.adapter
 
-import com.saveourtool.sarifutils.cli.config.FileReplacements
-import com.saveourtool.sarifutils.cli.config.RuleReplacements
-import com.saveourtool.sarifutils.cli.files.createTempDir
-import com.saveourtool.sarifutils.cli.files.fs
-import com.saveourtool.sarifutils.cli.files.readFile
-import com.saveourtool.sarifutils.cli.files.readLines
-import com.saveourtool.sarifutils.cli.files.writeContentWithNewLinesToFile
-import com.saveourtool.sarifutils.cli.utils.adaptedIsAbsolute
-import com.saveourtool.sarifutils.cli.utils.getUriBaseIdForArtifactLocation
-import com.saveourtool.sarifutils.cli.utils.resolveUriBaseId
+import com.saveourtool.sarifutils.config.FileReplacements
+import com.saveourtool.sarifutils.config.RuleReplacements
+import com.saveourtool.sarifutils.files.createTempDir
+import com.saveourtool.sarifutils.files.fs
+import com.saveourtool.sarifutils.files.readFile
+import com.saveourtool.sarifutils.files.readLines
+import com.saveourtool.sarifutils.files.writeContentWithNewLinesToFile
+import com.saveourtool.sarifutils.utils.adaptedIsAbsolute
+import com.saveourtool.sarifutils.utils.getUriBaseIdForArtifactLocation
+import com.saveourtool.sarifutils.utils.resolveUriBaseId
 import io.github.detekt.sarif4k.Replacement
 
 import io.github.detekt.sarif4k.Run

fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/cli/config/FileReplacements.kt → fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/config/FileReplacements.kt

@@ -1,4 +1,4 @@
-package com.saveourtool.sarifutils.cli.config
+package com.saveourtool.sarifutils.config
 
 import io.github.detekt.sarif4k.Replacement
 import okio.Path

fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/cli/files/FileUtils.kt → fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/files/FileUtils.kt

@@ -2,7 +2,7 @@
  * Utility methods to work with file system
  */
 
-package com.saveourtool.sarifutils.cli.files
+package com.saveourtool.sarifutils.files
 
 import okio.FileSystem
 import okio.Path

fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/cli/utils/SarifUtils.kt → fixpatches/src/commonMain/kotlin/com/saveourtool/sarifutils/utils/SarifUtils.kt

@@ -2,7 +2,7 @@
  * Utility methods to work with SARIF files.
  */
 
-package com.saveourtool.sarifutils.cli.utils
+package com.saveourtool.sarifutils.utils
 
 import io.github.detekt.sarif4k.ArtifactLocation
 import io.github.detekt.sarif4k.Result

fixpatches/src/commonTest/kotlin/com/saveourtool/sarifutils/adapter/SarifFixAdapterTest.kt

@@ -2,9 +2,8 @@
 
 package com.saveourtool.sarifutils.adapter
 
-import com.saveourtool.sarifutils.cli.adapter.SarifFixAdapter
-import com.saveourtool.sarifutils.cli.files.readFile
-import com.saveourtool.sarifutils.cli.files.readLines
+import com.saveourtool.sarifutils.files.readFile
+import com.saveourtool.sarifutils.files.readLines
 
 import io.github.detekt.sarif4k.Replacement
 import io.github.detekt.sarif4k.SarifSchema210

fixpatches/src/commonTest/kotlin/com/saveourtool/sarifutils/utils/SarifUtilsTest.kt

@@ -1,8 +1,5 @@
 package com.saveourtool.sarifutils.utils
 
-import com.saveourtool.sarifutils.cli.utils.getUriBaseIdForArtifactLocation
-import com.saveourtool.sarifutils.cli.utils.resolveUriBaseId
-
 import io.github.detekt.sarif4k.SarifSchema210
 import okio.Path
 import okio.Path.Companion.toPath

fixpatches/src/jvmMain/kotlin/com/saveourtool/sarifutils/cli/files/FileUtils.kt → fixpatches/src/jvmMain/kotlin/com/saveourtool/sarifutils/files/FileUtils.kt

@@ -4,7 +4,7 @@
 
 @file:JvmName("FileUtilsJvm")
 
-package com.saveourtool.sarifutils.cli.files
+package com.saveourtool.sarifutils.files
 
 import okio.FileSystem
 

fixpatches/src/nativeMain/kotlin/com/saveourtool/sarifutils/cli/files/FileUtils.kt → fixpatches/src/nativeMain/kotlin/com/saveourtool/sarifutils/files/FileUtils.kt

@@ -2,7 +2,7 @@
  * Utility methods to work with file system
  */
 
-package com.saveourtool.sarifutils.cli.files
+package com.saveourtool.sarifutils.files
 
 import okio.FileSystem